All Stories

  1. Rational design of glycosaminoglycan binding cyclic peptides using cPEPmatch

    Article • Computational and Structural Biotechnology Journal, December 2024, Elsevier

    Professor Martin Zacharias

  2. cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery

    Article • Computational and Structural Biotechnology Journal, December 2024, Elsevier

    Professor Martin Zacharias

  3. RNA dynamics from experimental and computational approaches

    Article • Structure, September 2024, Elsevier

    Professor Martin Zacharias

  4. Unraveling the mechanism of small molecule induced activation of Staphylococcus aureus signal peptidase IB

    Article • Communications Biology, July 2024, Springer Science + Business Media

    Professor Martin Zacharias

  5. Screening Privileged Alkyl Guanidinium Motifs under Host-Mimicking Conditions Reveals a Novel Antibiotic with an Unconventional Mode of Action

    Article • JACS Au, July 2024, American Chemical Society (ACS)

    Professor Martin Zacharias

  6. How arginine inhibits substrate‐binding domain 2 elucidated using molecular dynamics simulations

    Article • Protein Science, June 2024, Wiley

    Professor Martin Zacharias

  7. Helical reorganization in the context of membrane protein folding: Insights from simulations with bacteriorhodopsin (BR) fragments

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, June 2024, Elsevier

    Professor Martin Zacharias

  8. Structural Insights into Seeding Mechanisms of hIAPP Fibril Formation

    Article • Journal of the American Chemical Society, May 2024, American Chemical Society (ACS)

    Professor Martin Zacharias

  9. Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations

    Article • Journal of Chemical Information and Modeling, April 2024, American Chemical Society (ACS)

    Professor Martin Zacharias

  10. Peptide vaccines get an OS update

    Article • Nature Chemical Biology, April 2024, Springer Science + Business Media

    Professor Martin Zacharias

  11. Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation

    Article • Proteins Structure Function and Bioinformatics, March 2024, Wiley

    Professor Martin Zacharias

  12. Comprehensive Analysis of Coupled Proline Cis–Trans States in Bradykinin Using ωBP-REMD Simulations

    Article • Journal of Chemical Theory and Computation, March 2024, American Chemical Society (ACS)

    Professor Martin Zacharias

  13. Liquid–Vapor Coexistence and Spontaneous Evaporation at Atmospheric Pressure of Common Rigid Three-Point Water Models in Molecular Simulations

    Article • The Journal of Physical Chemistry B, March 2024, American Chemical Society (ACS)

    Professor Martin Zacharias

  14. The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics

    Article • Journal of Chemical Theory and Computation, February 2024, American Chemical Society (ACS)

    Professor Martin Zacharias

  15. Characterizing ATP processing by the AAA+ protein p97 at the atomic level

    Article • Nature Chemistry, February 2024, Springer Science + Business Media

    Professor Martin Zacharias

  16. Design of cyclic peptides as novel inhibitors of ICOS/ICOSL interaction

    Article • Bioorganic & Medicinal Chemistry Letters, February 2024, Elsevier

    Professor Martin Zacharias

  17. Refinement of Docked Protein-Protein Complexes Using Repulsive Scaling Replica Exchange Simulations

    Article • January 2024, Springer Science + Business Media

    Professor Martin Zacharias

  18. Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

    Article • Beilstein Journal of Organic Chemistry, December 2023, Beilstein Institut

    Professor Martin Zacharias

  19. How Modulator Binding at the Amyloidβ-γ-Secretase Interface Enhances Substrate Binding and Attenuates Membrane Distortion

    Article • Journal of Medicinal Chemistry, December 2023, American Chemical Society (ACS)

    Professor Martin Zacharias

  20. Assembly-dependent Structure Formation Shapes Human Interleukin-23 versus Interleukin-12 Secretion

    Article • Journal of Molecular Biology, December 2023, Elsevier

    Professor Martin Zacharias

  21. Efficient and accurate calculation of proline cis/trans isomerization free energies from Hamiltonian replica exchange molecular dynamics simulations

    Article • Structure, November 2023, Elsevier

    Professor Martin Zacharias

  22. The LytS-type histidine kinase BtsS is a 7-transmembrane receptor that binds pyruvate

    Article • mBio, October 2023, ASM Journals

    Professor Martin Zacharias

  23. APP substrate ectodomain defines amyloid‐β peptide length by restraining γ‐secretase processivity and facilitating product release

    Article • The EMBO Journal, October 2023, Springer Science + Business Media

    Professor Martin Zacharias

  24. APP substrate ectodomain defines Aβ length by restraining γ-secretase processivity and facilitating product release

    Article • September 2023, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  25. Coupling of conformation and CPD damage in nucleosomal DNA

    Article • Biophysical Chemistry, September 2023, Elsevier

    Professor Martin Zacharias

  26. Unravelling ATP processing by the AAA+ protein p97 at the atomic level

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  27. The development of nucleic acids force fields: From an unchallenged past to a competitive future

    Article • Biophysical Journal, July 2023, Elsevier

    Professor Martin Zacharias

  28. A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites

    Article • Angewandte Chemie International Edition, June 2023, Wiley

    Professor Martin Zacharias

  29. Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site

    Article • Communications Biology, June 2023, Springer Science + Business Media

    Professor Martin Zacharias

  30. Mechanistic insights into the aggregation pathway of the patient-derived immunoglobulin light chain variable domain protein FOR005

    Article • Nature Communications, June 2023, Springer Science + Business Media

    Professor Martin Zacharias

  31. Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21

    Article • Nature Structural & Molecular Biology, May 2023, Springer Science + Business Media

    Professor Martin Zacharias

  32. What Makes a Good Protein–Protein Interaction Stabilizer: Analysis and Application of the Dual-Binding Mechanism

    Article • ACS Central Science, April 2023, American Chemical Society (ACS)

    Professor Martin Zacharias

  33. A constant domain mutation in a patient-derived antibody light chain reveals principles of AL amyloidosis

    Article • Communications Biology, February 2023, Springer Science + Business Media

    Professor Martin Zacharias

  34. Toward Force Fields with Improved Base Stacking Descriptions

    Article • Journal of Chemical Theory and Computation, February 2023, American Chemical Society (ACS)

    Professor Martin Zacharias

  35. Water model determines thermosensitive and physicochemical properties of poly(N-isopropylacrylamide) in molecular simulations

    Article • Frontiers in Materials, January 2023, Frontiers

    Professor Martin Zacharias

  36. Mechanism of β‐hairpin formation in AzoChignolin and Chignolin

    Article • Journal of Computational Chemistry, December 2022, Wiley

    Professor Martin Zacharias

  37. Benchmarking biomolecular force field‐based Zn2+ for mono‐ and bimetallic ligand binding sites

    Article • Journal of Computational Chemistry, December 2022, Wiley

    Professor Martin Zacharias

  38. The human signal peptidase complex acts as a quality control enzyme for membrane proteins

    Article • Science, December 2022, American Association for the Advancement of Science

    Professor Martin Zacharias

  39. Amyloid fibril structure from the vascular variant of systemic AA amyloidosis

    Article • Nature Communications, November 2022, Springer Science + Business Media

    Professor Martin Zacharias

  40. Fast peptide exchange on major histocompatibility complex class I molecules by acidic stabilization of a peptide‐empty intermediate

    Article • Protein Science, November 2022, Wiley

    Professor Martin Zacharias

  41. Intramembrane client recognition potentiates the chaperone functions of calnexin

    Article • The EMBO Journal, October 2022, Springer Science + Business Media

    Professor Martin Zacharias

  42. Enzyme–substrate interface targeting by imidazole‐based γ‐secretase modulators activates γ‐secretase and stabilizes its interaction withAPP

    Article • The EMBO Journal, September 2022, Springer Science + Business Media

    Professor Martin Zacharias

  43. Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function

    Article • Science Advances, September 2022, American Association for the Advancement of Science

    Professor Martin Zacharias

  44. Analysis of amyloidogenic transthyretin mutations using continuum solvent free energy calculations

    Article • Proteins Structure Function and Bioinformatics, August 2022, Wiley

    Professor Martin Zacharias

  45. Mechanistic insight into the aggregation pathway of an immunoglobulin light chain protein

    Article • July 2022, Research Square

    Professor Martin Zacharias

  46. Case Report: DPM1-CDG: Novel Variant with Severe Phenotype and Literature Review

    Article • Frontiers in Genetics, July 2022, Frontiers

    Professor Martin Zacharias

  47. Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock

    Article • Journal of Chemical Information and Modeling, July 2022, American Chemical Society (ACS)

    Professor Martin Zacharias

  48. Explicit solvent repulsive scaling replica exchange molecular dynamics (RS‐REMD) in molecular modeling of protein‐glycosaminoglycan complexes

    Article • Journal of Computational Chemistry, July 2022, Wiley

    Professor Martin Zacharias

  49. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications

    Article • Journal of Chemical Theory and Computation, June 2022, American Chemical Society (ACS)

    Professor Martin Zacharias

  50. An internal docking site stabilizes substrate binding to γ-secretase: Analysis by molecular dynamics simulations

    Article • Biophysical Journal, June 2022, Elsevier

    Professor Martin Zacharias

  51. ADAMTS4-specific MR probe to assess aortic aneurysms in vivo using synthetic peptide libraries

    Article • Nature Communications, May 2022, Springer Science + Business Media

    Professor Martin Zacharias

  52. Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis

    Article • eLife, May 2022, eLife

    Professor Martin Zacharias

  53. Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations

    Article • The Journal of Physical Chemistry B, May 2022, American Chemical Society (ACS)

    Professor Martin Zacharias

  54. Dissociation of β2m from MHC class I triggers formation of noncovalent transient heavy chain dimers

    Article • Journal of Cell Science, May 2022, The Company of Biologists

    Professor Martin Zacharias

  55. Intra-membrane client recognition potentiates the chaperone functions of Calnexin

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  56. Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  57. Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding

    Article • Nature Communications, January 2022, Springer Science + Business Media

    Professor Martin Zacharias

  58. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA

    Article • Computational and Structural Biotechnology Journal, January 2022, Elsevier

    Professor Martin Zacharias

  59. Rapid Rational Design of Cyclic Peptides Mimicking Protein–Protein Interfaces

    Article • January 2022, Springer Science + Business Media

    Professor Martin Zacharias

  60. Rapid peptide exchange on MHC class I by small molecules elucidates dynamics of bound peptide

    Article • Current Research in Immunology, January 2022, Elsevier

    Professor Martin Zacharias

  61. Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations

    Article • The Journal of Physical Chemistry B, December 2021, American Chemical Society (ACS)

    Professor Martin Zacharias

  62. Structural dynamics in the evolution of a bilobed protein scaffold

    Article • Proceedings of the National Academy of Sciences, November 2021, Proceedings of the National Academy of Sciences

    Professor Martin Zacharias

  63. Binding-induced functional-domain motions in the Argonaute characterized by adaptive advanced sampling

    Article • PLoS Computational Biology, November 2021, PLOS

    Professor Martin Zacharias

  64. Mechanistic principles of an ultra-long bovine CDR reveal strategies for antibody design

    Article • Nature Communications, November 2021, Springer Science + Business Media

    Professor Martin Zacharias

  65. Match_Motif: A rapid computational tool to assist in protein–protein interaction design

    Article • Protein Science, October 2021, Wiley

    Professor Martin Zacharias

  66. Tumuc1: A New Accurate DNA Force Field Consistent with High-Level Quantum Chemistry

    Article • Journal of Chemical Theory and Computation, October 2021, American Chemical Society (ACS)

    Professor Martin Zacharias

  67. Modeling Protein–Glycosaminoglycan Complexes: Does the Size Matter?

    Article • Journal of Chemical Information and Modeling, September 2021, American Chemical Society (ACS)

    Professor Martin Zacharias

  68. Molecular insights on CALX-CBD12 interdomain dynamics from MD simulations, RDCs, and SAXS

    Article • Biophysical Journal, September 2021, Elsevier

    Professor Martin Zacharias

  69. Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series

    Article • ChemPhysChem, August 2021, Wiley

    Professor Martin Zacharias

  70. Dissociation of β2m from MHC Class I Triggers Formation of Noncovalent, Transient Heavy Chain Dimers

    Article • July 2021, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  71. Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series**

    Article • ChemPhysChem, June 2021, Wiley

    Professor Martin Zacharias

  72. Mechanism of collagen folding propagation studied by Molecular Dynamics simulations

    Article • PLoS Computational Biology, June 2021, PLOS

    Professor Martin Zacharias

  73. Influence of a Ser111‐phosphorylation on Rab1b GTPase conformational dynamics studied by advanced sampling simulations

    Article • Proteins Structure Function and Bioinformatics, June 2021, Wiley

    Professor Martin Zacharias

  74. Computational Tools for Accurate Binding Free-Energy Prediction

    Article • May 2021, Springer Science + Business Media

    Professor Martin Zacharias

  75. Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts

    Article • Crystals, May 2021, MDPI AG

    Professor Martin Zacharias

  76. Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD

    Article • Nature Communications, April 2021, Springer Science + Business Media

    Professor Martin Zacharias

  77. Accurate modeling of DNA conformational flexibility by a multivariate Ising model

    Article • Proceedings of the National Academy of Sciences, April 2021, Proceedings of the National Academy of Sciences

    Professor Martin Zacharias

  78. Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans

    Article • Journal of Computational Chemistry, March 2021, Wiley

    Professor Martin Zacharias

  79. Molecular mechanism of amyloidogenic mutations in hypervariable regions of antibody light chains

    Article • Journal of Biological Chemistry, January 2021, Elsevier

    Professor Martin Zacharias

  80. Proteolysis of Rab32 by Salmonella GtgE induces an inactive GTPase conformation

    Article • iScience, January 2021, Elsevier

    Professor Martin Zacharias

  81. Targeting Telomeres: Molecular Dynamics and Free Energy Simulation of Gold-Carbene Binding to DNA

    Article • Biophysical Journal, January 2021, Elsevier

    Professor Martin Zacharias

  82. Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  83. Altered Hinge Conformations in APP Transmembrane Helix Mutants May Affect Enzyme–Substrate Interactions of γ-Secretase

    Article • ACS Chemical Neuroscience, November 2020, American Chemical Society (ACS)

    Professor Martin Zacharias

  84. Molecular and spectroscopic characterization of green and red cyanine fluorophores from the Alexa Fluor and AF series

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  85. Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation

    Article • The Journal of Physical Chemistry B, November 2020, American Chemical Society (ACS)

    Professor Martin Zacharias

  86. Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations

    Article • Protein Science, November 2020, Wiley

    Professor Martin Zacharias

  87. Efficient Refinement and Free Energy Scoring of Predicted Protein–Protein Complexes Using Replica Exchange with Repulsive Scaling

    Article • Journal of Chemical Information and Modeling, October 2020, American Chemical Society (ACS)

    Professor Martin Zacharias

  88. Evolution of structural dynamics in bilobed proteins

    Article • October 2020, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  89. Rapid in silico Design of Potential Cyclic Peptide Binders Targeting Protein-Protein Interfaces

    Article • Frontiers in Chemistry, October 2020, Frontiers

    Professor Martin Zacharias

  90. How Mutations Perturb γ-Secretase Active Site Studied by Free Energy Simulations

    Article • ACS Chemical Neuroscience, September 2020, American Chemical Society (ACS)

    Professor Martin Zacharias

  91. The dynamics of γ-secretase and its substrates

    Article • Seminars in Cell and Developmental Biology, September 2020, Elsevier

    Professor Martin Zacharias

  92. Base pairing and stacking contributions to double stranded DNA formation

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  93. From monomer to fibril: Abeta‐amyloid binding to Aducanumab antibody studied by molecular dynamics simulation

    Article • Proteins Structure Function and Bioinformatics, August 2020, Wiley

    Professor Martin Zacharias

  94. CHARMM-GUI supports the Amber force fields

    Article • The Journal of Chemical Physics, July 2020, American Institute of Physics

    Professor Martin Zacharias

  95. Folding and Unfolding of the Short Light-Triggered β-Hairpin Peptide AzoChignolin Occurs within 100 ns

    Article • The Journal of Physical Chemistry B, June 2020, American Chemical Society (ACS)

    Professor Martin Zacharias

  96. How global DNA unwinding causes non-uniform stress distribution and melting of DNA

    Article • PLoS ONE, May 2020, PLOS

    Professor Martin Zacharias

  97. NWChem: Past, present, and future

    Article • The Journal of Chemical Physics, May 2020, American Institute of Physics

    Prof. Yan Zhao, Professor Martin Zacharias

  98. Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation

    Article • Journal of Chemical Theory and Computation, March 2020, American Chemical Society (ACS)

    Professor Martin Zacharias

  99. Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection

    Article • Nature Communications, March 2020, Springer Science + Business Media

    Professor Martin Zacharias

  100. Fatal amyloid formation in a patient’s antibody light chain is caused by a single point mutation

    Article • eLife, March 2020, eLife

    Professor Martin Zacharias

  101. Prediction of protein–protein complexes using replica exchange with repulsive scaling

    Article • Journal of Computational Chemistry, March 2020, Wiley

    Professor Martin Zacharias

  102. Molecular mechanism of Be2+-ion binding to HLA-DP2: tetrahedral coordination, conformational changes and multi-ion binding

    Article • Physical Chemistry Chemical Physics, January 2020, Royal Society of Chemistry

    Professor Martin Zacharias

  103. Coarse‐grained and atomic resolution biomolecular docking with the ATTRACT approach

    Article • Proteins Structure Function and Bioinformatics, December 2019, Wiley

    Professor Martin Zacharias

  104. The structure and oxidation of the eye lens chaperone αA-crystallin

    Article • Nature Structural & Molecular Biology, December 2019, Springer Science + Business Media

    Professor Martin Zacharias

  105. Cryo-EM structure of a transthyretin-derived amyloid fibril from a patient with hereditary ATTR amyloidosis

    Article • Nature Communications, November 2019, Springer Science + Business Media

    Professor Martin Zacharias

  106. Computational prediction of protein–protein binding affinities

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, October 2019, Wiley

    Professor Martin Zacharias

  107. Global Dynamics of Yeast Hsp90 Middle and C-Terminal Dimer Studied by Advanced Sampling Simulations

    Article • Frontiers in Molecular Biosciences, September 2019, Frontiers

    Professor Martin Zacharias

  108. The Architecture of Talin1 Reveals an Autoinhibition Mechanism

    Article • Cell, September 2019, Elsevier

    Professor Martin Zacharias

  109. Phosphorylation of Ser111 in Rab8a Modulates Rabin8-Dependent Activation by Perturbation of Side Chain Interaction Networks

    Article • Biochemistry, July 2019, American Chemical Society (ACS)

    Professor Martin Zacharias

  110. Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells

    Article • Science Immunology, July 2019, American Association for the Advancement of Science

    Professor Martin Zacharias

  111. Uncovering the Binding Mode of γ -Secretase Inhibitors

    Article • ACS Chemical Neuroscience, June 2019, American Chemical Society (ACS)

    Professor Martin Zacharias

  112. Phosphorylation of Ser111 in Rab8a modulates Rabin8 dependent activation by perturbation of side chain interaction networks

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  113. Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ‐secretase modulators

    Article • The EMBO Journal, May 2019, Springer Science + Business Media

    Professor Martin Zacharias

  114. An Interspecies Analysis Reveals Molecular Construction Principles of Interleukin 27

    Article • Journal of Molecular Biology, May 2019, Elsevier

    Professor Martin Zacharias

  115. Free energy calculations elucidate substrate binding, gating mechanism, and tolerance‐promoting mutations in herbicide target 4‐hydroxyphenylpyruvate dioxygenase

    Article • Protein Science, April 2019, Wiley

    Professor Martin Zacharias

  116. Uncovering the Binding Mode of γ-Secretase Inhibitors

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  117. Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations

    Article • Angewandte Chemie International Edition, March 2019, Wiley

    Professor Martin Zacharias

  118. Computer Modelling and Molecular Dynamics Simulation of Biomolecules

    Article • March 2019, Wiley

    Professor Martin Zacharias

  119. Dynamics of the full-length yeast Hsp90 dimer

    Article • The European Physical Journal Special Topics, March 2019, Springer Science + Business Media

    Professor Martin Zacharias

  120. Modeling large protein–glycosaminoglycan complexes using a fragment‐based approach

    Article • Journal of Computational Chemistry, February 2019, Wiley

    Professor Martin Zacharias

  121. Evaluation of Predicted Protein–Protein Complexes by Binding Free Energy Simulations

    Article • Journal of Chemical Theory and Computation, January 2019, American Chemical Society (ACS)

    Professor Martin Zacharias

  122. A folding switch regulates interleukin 27 biogenesis and secretion of its α-subunit as a cytokine

    Article • Proceedings of the National Academy of Sciences, January 2019, Proceedings of the National Academy of Sciences

    Professor Martin Zacharias

  123. Structural Modeling of γ-Secretase Aβn Complex Formation and Substrate Processing

    Article • ACS Chemical Neuroscience, January 2019, American Chemical Society (ACS)

    Professor Martin Zacharias

  124. γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding

    Article • Frontiers in Chemistry, January 2019, Frontiers

    Professor Martin Zacharias

  125. The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding

    Article • Journal of Molecular Biology, January 2019, Elsevier

    Professor Martin Zacharias

  126. Structural Modeling of γ-Secretase Aβn Complex Formation and Substrate Processing

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  127. How methyl–sugar interactions determine DNA structure and flexibility

    Article • Nucleic Acids Research, December 2018, Oxford University Press (OUP)

    Professor Martin Zacharias

  128. A single residue switch reveals principles of antibody domain integrity

    Article • Journal of Biological Chemistry, November 2018, Elsevier

    Professor Martin Zacharias

  129. Designed Macrocyclic Peptides as Nanomolar Amyloid Inhibitors Based on Minimal Recognition Elements

    Article • Angewandte Chemie International Edition, July 2018, Wiley

    Professor Martin Zacharias

  130. The temperature dependence of the helical twist of DNA

    Article • Nucleic Acids Research, July 2018, Oxford University Press (OUP)

    Professor Martin Zacharias

  131. Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices

    Article • Proceedings of the National Academy of Sciences, July 2018, Proceedings of the National Academy of Sciences

    Professor Martin Zacharias

  132. Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling

    Article • Structure, February 2018, Elsevier

    Professor Martin Zacharias

  133. Unwinding Induced Melting of Double-Stranded DNA Studied by Free Energy Simulations

    Article • The Journal of Physical Chemistry B, November 2017, American Chemical Society (ACS)

    Professor Martin Zacharias

  134. Comparative Molecular Dynamics Analysis of RNase-S Complex Formation

    Article • Biophysical Journal, October 2017, Elsevier

    Professor Martin Zacharias

  135. Determinants of the assembly and function of antibody variable domains

    Article • Scientific Reports, September 2017, Springer Science + Business Media

    Professor Martin Zacharias

  136. Multiscale Simulation of Receptor–Drug Association Kinetics: Application to Neuraminidase Inhibitors

    Article • Journal of Chemical Theory and Computation, September 2017, American Chemical Society (ACS)

    Professor Martin Zacharias

  137. Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly

    Article • Journal of Biological Chemistry, September 2017, Elsevier

    Professor Martin Zacharias

  138. Update of the ATTRACT force field for the prediction of protein-protein binding affinity

    Article • Journal of Computational Chemistry, June 2017, Wiley

    Professor Martin Zacharias

  139. Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations

    Article • Biophysical Journal, June 2017, Elsevier

    Professor Martin Zacharias

  140. Covalent dye attachment influences the dynamics and conformational properties of flexible peptides

    Article • PLoS ONE, May 2017, PLOS

    Professor Martin Zacharias

  141. Thermodynamics and Kinetics of Nucleobase Stacking Oligomerization Revealed by Molecular Dynamics Simulations

    Article • Journal of Chemical Theory and Computation, May 2017, American Chemical Society (ACS)

    Professor Martin Zacharias

  142. Fast and accurate grid representations for atom‐based docking with partner flexibility

    Article • Journal of Computational Chemistry, May 2017, Wiley

    Professor Martin Zacharias

  143. The pepATTRACT web server for blind, large-scale peptide–protein docking

    Article • Nucleic Acids Research, April 2017, Oxford University Press (OUP)

    Professor Martin Zacharias

  144. Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations

    Article • PLoS ONE, March 2017, PLOS

    Professor Martin Zacharias

  145. Predicting Allosteric Changes from Conformational Ensembles

    Article • Structure, March 2017, Elsevier

    Professor Martin Zacharias

  146. Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential

    Article • PLoS ONE, February 2017, PLOS

    Professor Martin Zacharias

  147. Monte Carlo replica-exchange based ensemble docking of protein conformations

    Article • Proteins Structure Function and Bioinformatics, February 2017, Wiley

    Professor Martin Zacharias

  148. Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage

    Article • Scientific Reports, January 2017, Springer Science + Business Media

    Professor Martin Zacharias

  149. Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking

    Article • PLoS ONE, January 2017, PLOS

    Professor Martin Zacharias

  150. Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail

    Article • eLife, January 2017, eLife

    Professor Martin Zacharias

  151. From Aβ Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations

    Article • The Journal of Physical Chemistry B, January 2017, American Chemical Society (ACS)

    Professor Martin Zacharias

  152. Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions

    Article • January 2017, Springer Science + Business Media

    Professor Martin Zacharias

  153. Optical control of a receptor-linked guanylyl cyclase using a photoswitchable peptidic hormone

    Article • Chemical Science, January 2017, Royal Society of Chemistry

    Professor Martin Zacharias

  154. Multidomain structure and correlated dynamics determined by self-consistent FRET networks

    Article • Nature Methods, December 2016, Springer Science + Business Media

    Professor Martin Zacharias

  155. Protein‐protein and peptide‐protein docking and refinement using ATTRACT in CAPRI

    Article • Proteins Structure Function and Bioinformatics, November 2016, Wiley

    Professor Martin Zacharias

  156. Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by Phosphorylation

    Article • The Journal of Physical Chemistry B, November 2016, American Chemical Society (ACS)

    Professor Martin Zacharias

  157. Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DNA

    Article • Nucleic Acids Research, September 2016, Oxford University Press (OUP)

    Professor Martin Zacharias

  158. Single-molecule dissection of stacking forces in DNA

    Article • Science, September 2016, American Association for the Advancement of Science

    Professor Martin Zacharias

  159. Structure and target interaction of a G-quadruplex RNA-aptamer

    Article • RNA Biology, August 2016, Taylor & Francis

    Professor Martin Zacharias

  160. SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes

    Article • Structure, August 2016, Elsevier

    Professor Martin Zacharias

  161. Free energy analysis and mechanism of base pair stacking in nicked DNA

    Article • Nucleic Acids Research, July 2016, Oxford University Press (OUP)

    Professor Martin Zacharias

  162. Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules

    Article • Journal of Computational Chemistry, May 2016, Wiley

    Professor Martin Zacharias

  163. Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

    Article • Nucleic Acids Research, April 2016, Oxford University Press (OUP)

    Professor Martin Zacharias

  164. Mechanism of pKID/KIX Association Studied by Molecular Dynamics Free Energy Simulations

    Article • The Journal of Physical Chemistry B, April 2016, American Chemical Society (ACS)

    Professor Martin Zacharias

  165. Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins

    Article • Journal of Molecular Biology, April 2016, Elsevier

    Professor Martin Zacharias

  166. A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions

    Article • Journal of Molecular Biology, March 2016, Elsevier

    Professor Martin Zacharias

  167. Subnanometre enzyme mechanics probed by single-molecule force spectroscopy

    Article • Nature Communications, February 2016, Springer Science + Business Media

    Professor Martin Zacharias

  168. Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling

    Article • Biophysical Journal, February 2016, Elsevier

    Professor Martin Zacharias

  169. Adenylylation of Tyr77 stabilizes Rab1b GTPase in an active state: A molecular dynamics simulation analysis

    Article • Scientific Reports, January 2016, Springer Science + Business Media

    Professor Martin Zacharias

  170. Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

    Article • PLoS Computational Biology, January 2016, PLOS

    Professor Martin Zacharias

  171. Mechanism of Reversible Peptide–Bilayer Attachment: Combined Simulation and Experimental Single-Molecule Study

    Article • Langmuir, January 2016, American Chemical Society (ACS)

    Professor Martin Zacharias

  172. Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step

    Article • Journal of the American Chemical Society, January 2016, American Chemical Society (ACS)

    Professor Martin Zacharias

  173. The Antibody Light-Chain Linker Is Important for Domain Stability and Amyloid Formation

    Article • Journal of Molecular Biology, November 2015, Elsevier

    Professor Martin Zacharias

  174. Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase

    Article • Biophysical Journal, November 2015, Elsevier

    Professor Martin Zacharias

  175. Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis

    Article • Nucleic Acids Research, October 2015, Oxford University Press (OUP)

    Professor Martin Zacharias

  176. RAID3 - An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity

    Article • RNA Biology, September 2015, Taylor & Francis

    Professor Martin Zacharias

  177. The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study

    Article • PLoS ONE, August 2015, PLOS

    Professor Martin Zacharias

  178. Fully Blind Peptide-Protein Docking with pepATTRACT

    Article • Structure, August 2015, Elsevier

    Professor Martin Zacharias

  179. Exploring biomolecular dynamics and interactions using advanced sampling methods

    Article • Journal of Physics Condensed Matter, July 2015, Institute of Physics Publishing

    Professor Martin Zacharias

  180. Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta

    Article • PLoS ONE, June 2015, PLOS

    Professor Martin Zacharias

  181. An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA

    Article • PLoS ONE, March 2015, PLOS

    Professor Martin Zacharias

  182. A Compact Native 24-Residue Supersecondary Structure Derived from the Villin Headpiece Subdomain

    Article • Biophysical Journal, February 2015, Elsevier

    Professor Martin Zacharias

  183. A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT

    Article • Biophysical Journal, February 2015, Elsevier

    Professor Martin Zacharias

  184. Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations

    Article • Molecular Immunology, February 2015, Elsevier

    Professor Martin Zacharias

  185. Influence of a cis,syn‐cyclobutane pyrimidine dimer damage on DNA conformation studied by molecular dynamics simulations

    Article • Biopolymers, January 2015, Wiley

    Professor Martin Zacharias

  186. iATTRACT: Simultaneous global and local interface optimization for protein–protein docking refinement

    Article • Proteins Structure Function and Bioinformatics, December 2014, Wiley

    Professor Martin Zacharias

  187. Effect O6‐guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations

    Article • Biopolymers, October 2014, Wiley

    Professor Martin Zacharias

  188. Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations

    Article • Proteins Structure Function and Bioinformatics, October 2014, Wiley

    Professor Martin Zacharias

  189. Efficient calculation of relative binding free energies by umbrella sampling perturbation

    Article • Journal of Computational Chemistry, September 2014, Wiley

    Professor Martin Zacharias

  190. Rapid Alchemical Free Energy Calculation Employing a Generalized Born Implicit Solvent Model

    Article • The Journal of Physical Chemistry B, September 2014, American Chemical Society (ACS)

    Professor Martin Zacharias

  191. A Residue-specific Shift in Stability and Amyloidogenicity of Antibody Variable Domains

    Article • Journal of Biological Chemistry, September 2014, Elsevier

    Professor Martin Zacharias

  192. Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations

    Article • The Journal of Physical Chemistry B, June 2014, American Chemical Society (ACS)

    Professor Martin Zacharias

  193. Protein–Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials

    Article • Journal of Chemical Information and Modeling, June 2014, American Chemical Society (ACS)

    Professor Martin Zacharias

  194. PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

    Article • Nucleic Acids Research, May 2014, Oxford University Press (OUP)

    Professor Martin Zacharias

  195. Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

    Article • PLoS ONE, February 2014, PLOS

    Professor Martin Zacharias

  196. Stabilization of duplex DNA and RNA by dangling ends studied by free energy simulations

    Article • Biopolymers, January 2014, Wiley

    Professor Martin Zacharias

  197. Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations

    Article • Journal of Chemical Theory and Computation, January 2014, American Chemical Society (ACS)

    Professor Martin Zacharias

  198. A Novel Family of Human Leukocyte Antigen Class II Receptors May Have Its Origin in Archaic Human Species

    Article • Journal of Biological Chemistry, January 2014, Elsevier

    Professor Martin Zacharias

  199. Computational Antigenic Epitope Prediction by Calculating Electrostatic Desolvation Penalties of Protein Surfaces

    Article • January 2014, Springer Science + Business Media

    Professor Martin Zacharias

  200. Blind prediction of interfacial water positions in CAPRI

    Article • Proteins Structure Function and Bioinformatics, November 2013, Wiley

    Dr. Alexandre M.J.J. Bonvin, Professor Martin Zacharias

  201. Elastic Network Models of Nucleic Acids Flexibility

    Article • Journal of Chemical Theory and Computation, November 2013, American Chemical Society (ACS)

    Professor Martin Zacharias

  202. Crystal Structures of the Free and Ligand-Bound FK1–FK2 Domain Segment of FKBP52 Reveal a Flexible Inter-Domain Hinge

    Article • Journal of Molecular Biology, November 2013, Elsevier

    Dr. Andreas Bracher, Professor Martin Zacharias

  203. Hamiltonian replica‐exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles

    Article • Journal of Computational Chemistry, October 2013, Wiley

    Professor Martin Zacharias

  204. Flexible docking and refinement with a coarse‐grained protein model using ATTRACT

    Article • Proteins Structure Function and Bioinformatics, October 2013, Wiley

    Professor Martin Zacharias

  205. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

    Article • Glycobiology, October 2013, Oxford University Press (OUP)

    Professor Martin Zacharias

  206. Mapping the Spatial Neighborhood of the Regulatory 6S RNA Bound to Escherichia coli RNA Polymerase Holoenzyme

    Article • Journal of Molecular Biology, October 2013, Elsevier

    Professor Martin Zacharias

  207. Effect of 8-Oxoguanine on DNA Structure and Deformability

    Article • The Journal of Physical Chemistry B, September 2013, American Chemical Society (ACS)

    Professor Martin Zacharias

  208. Dipeptides promote folding and peptide binding of MHC class I molecules

    Article • Proceedings of the National Academy of Sciences, September 2013, Proceedings of the National Academy of Sciences

    Professor Martin Zacharias

  209. Redirecting catalysis from proteolysis to perhydrolysis in subtilisin Carlsberg

    Article • Journal of Biotechnology, September 2013, Elsevier

    Professor Martin Zacharias

  210. Proline substitution independently enhances H‐2Db complex stabilization and TCR recognition of melanoma‐associated peptides

    Article • European Journal of Immunology, August 2013, Wiley

    Professor Martin Zacharias

  211. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

    Article • Proteins Structure Function and Bioinformatics, August 2013, Wiley

    Dr. Alexandre M.J.J. Bonvin, Professor Martin Zacharias

  212. Theoretical studies of nucleic acids folding

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, July 2013, Wiley

    Professor Martin Zacharias

  213. Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus

    Article • PLoS Computational Biology, June 2013, PLOS

    Professor Martin Zacharias

  214. Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins

    Article • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, May 2013, Elsevier

    Professor Martin Zacharias

  215. A family of macrodomain proteins reverses cellular mono-ADP-ribosylation

    Article • Nature Structural & Molecular Biology, March 2013, Springer Science + Business Media

    Professor Martin Zacharias

  216. Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations

    Article • Biophysical Journal, March 2013, Elsevier

    Professor Martin Zacharias

  217. gp130 activation is regulated by D2–D3 interdomain connectivity

    Article • Biochemical Journal, February 2013, Portland Press Ltd.

    Professor Martin Zacharias

  218. Transformations in plasma membranes of cancerous cells and resulting consequences for cation insertion studied with molecular dynamics

    Article • Physical Chemistry Chemical Physics, January 2013, Royal Society of Chemistry

    Professor Martin Zacharias

  219. ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps

    Article • PLoS ONE, December 2012, PLOS

    Professor Martin Zacharias

  220. Reengineering of subtilisin Carlsberg for oxidative resistance

    Article • Biological Chemistry, December 2012, De Gruyter

    Professor Martin Zacharias

  221. Combining geometric pocket detection and desolvation properties to detect putative ligand binding sites on proteins

    Article • Journal of Structural Biology, December 2012, Elsevier

    Professor Martin Zacharias

  222. Role of tyrosine hot‐spot residues at the interface of colicin E9 and immunity protein 9: A comparative free energy simulation study

    Article • Proteins Structure Function and Bioinformatics, November 2012, Wiley

    Professor Martin Zacharias

  223. ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease

    Article • PLoS ONE, October 2012, PLOS

    Professor Martin Zacharias

  224. Combining coarse‐grained nonbonded and atomistic bonded interactions for protein modeling

    Article • Proteins Structure Function and Bioinformatics, September 2012, Wiley

    Professor Martin Zacharias

  225. Protein-DNA docking with a coarse-grained force field

    Article • BMC Bioinformatics, September 2012, Springer Science + Business Media

    Professor Martin Zacharias

  226. DNA Interaction of the CcrM DNA Methyltransferase: A Mutational and Modeling Study

    Article • ChemBioChem, May 2012, Wiley

    Professor Albert Jeltsch, Professor Martin Zacharias

  227. Atomic resolution model of the antibody Fc interaction with the complement C1q component

    Article • Molecular Immunology, May 2012, Elsevier

    Professor Martin Zacharias

  228. New insights into the role of the glutamic acid of the E‐box motif in group B Streptococcus pilus 2a assembly

    Article • The FASEB Journal, January 2012, Wiley

    Professor Martin Zacharias

  229. Molecular Dynamics and Advanced Sampling Simulations of Nucleic Acids

    Article • January 2012, Springer Science + Business Media

    Professor Martin Zacharias

  230. Scoring optimisation of unbound protein–protein docking including protein binding site predictions

    Article • Journal of Molecular Recognition, December 2011, Wiley

    Professor Martin Zacharias

  231. Multiple molecular architectures of the eye lens chaperone αB-crystallin elucidated by a triple hybrid approach

    Article • Proceedings of the National Academy of Sciences, December 2011, Proceedings of the National Academy of Sciences

    Professor Martin Zacharias

  232. ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking

    Article • November 2011, Springer Science + Business Media

    Professor Martin Zacharias

  233. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

    Article • Journal of Molecular Biology, November 2011, Elsevier

    Professor Yaoqi Zhou, Dr. Alexandre M.J.J. Bonvin, Professor Martin Zacharias

  234. Flexible Protein-Protein Docking

    Article • October 2011, IntechOpen

    Professor Martin Zacharias

  235. Efficient inclusion of receptor flexibility in grid‐based protein–ligand docking*

    Article • Journal of Computational Chemistry, September 2011, Wiley

    Professor Martin Zacharias

  236. A coarse-grained force field for Protein–RNA docking

    Article • Nucleic Acids Research, August 2011, Oxford University Press (OUP)

    Professor Martin Zacharias

  237. Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility

    Article • The FASEB Journal, August 2011, Wiley

    Professor Martin Zacharias

  238. Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations

    Article • Nucleic Acids Research, June 2011, Oxford University Press (OUP)

    Professor Martin Zacharias

  239. Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations

    Article • Journal of the American Chemical Society, June 2011, American Chemical Society (ACS)

    Professor Martin Zacharias

  240. Cytokine-induced Paracrystals Prolong the Activity of Signal Transducers and Activators of Transcription (STAT) and Provide a Model for the Regulation of Protein Solubility by Small Ubiquitin-like Modifier (SUMO)

    Article • Journal of Biological Chemistry, May 2011, Elsevier

    Professor Martin Zacharias

  241. Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent

    Article • Journal of Cheminformatics, April 2011, Springer Science + Business Media

    Professor Martin Zacharias

  242. Stoichiometry of HLA Class II-Invariant Chain Oligomers

    Article • PLoS ONE, February 2011, PLOS

    Professor Martin Zacharias

  243. Exploiting Antigenic Diversity for Vaccine Design

    Article • Journal of Biological Chemistry, September 2010, Elsevier

    Professor Martin Zacharias

  244. Application of biasing‐potential replica‐exchange simulations for loop modeling and refinement of proteins in explicit solvent

    Article • Proteins Structure Function and Bioinformatics, August 2010, Wiley

    Professor Martin Zacharias

  245. EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

    Article • BMC Bioinformatics, July 2010, Springer Science + Business Media

    Professor Martin Zacharias

  246. Syntheses and activities of backbone‐side chain cyclic octapeptide ligands with N‐functionalized phosphotyrosine for the N‐terminal SH2‐domain of the protein tyrosine phosphatase SHP‐1

    Article • Journal of Peptide Science, July 2010, Wiley

    Professor Martin Zacharias

  247. Synthetic Strategies to a Backbone-Side Chain Cyclic SHP-1 N-SH2 Ligand Containing N-Functionalized Alkyl Phosphotyrosine

    Article • Protein and Peptide Letters, July 2010, Bentham Science Publishers

    Professor Martin Zacharias

  248. Binding site prediction and improved scoring during flexible protein–protein docking with ATTRACT

    Article • Proteins Structure Function and Bioinformatics, June 2010, Wiley

    Professor Martin Zacharias

  249. Hydration in Discrete Water. A Mean Field, Cellular Automata Based Approach to Calculating Hydration Free Energies

    Article • The Journal of Physical Chemistry B, June 2010, American Chemical Society (ACS)

    Professor Martin Zacharias

  250. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

    Article • Nucleic Acids Research, May 2010, Oxford University Press (OUP)

    Professor Martin Zacharias

  251. In Silico Prediction of Binding Sites on Proteins

    Article • Current Medicinal Chemistry, May 2010, Bentham Science Publishers

    Professor Martin Zacharias

  252. Protein-Protein Complexes

    Article • May 2010, World Scientific Pub Co Pte Lt

    Professor Martin Zacharias

  253. Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

    Article • Biophysical Journal, May 2010, Elsevier

    Professor Martin Zacharias

  254. Accounting for conformational changes during protein–protein docking

    Article • Current Opinion in Structural Biology, April 2010, Elsevier

    Professor Martin Zacharias

  255. Tackling the challenges posed by target flexibility in drug design

    Article • Expert Opinion on Drug Discovery, March 2010, Informa Healthcare

    Professor Martin Zacharias

  256. Examining the potency of suggested inhibitors for the phosphatase activity of the human soluble epoxide hydrolase by molecular dynamics simulations

    Article • Journal of Molecular Structure THEOCHEM, March 2010, Elsevier

    Professor Martin Zacharias

  257. Bovine Serum Albumin and Lysozyme Adsorption on Calcium Phosphate Particles

    Article • Advanced Engineering Materials, February 2010, Wiley

    Professor Martin Zacharias

  258. Peptide binding to MHC class I and II proteins: New avenues from new methods

    Article • Molecular Immunology, January 2010, Elsevier

    Professor Martin Zacharias

  259. Binding of the Bacteriophage P22 N-Peptide to the boxB RNA Motif Studied by Molecular Dynamics Simulations

    Article • Biophysical Journal, December 2009, Elsevier

    Professor Martin Zacharias

  260. Elbow Flexibility of the kt38 RNA Kink-Turn Motif Investigated by Free-Energy Molecular Dynamics Simulations

    Article • Biophysical Journal, October 2009, Elsevier

    Professor Martin Zacharias

  261. Prediction of antigenic epitopes on protein surfaces by consensus scoring

    Article • BMC Bioinformatics, September 2009, Springer Science + Business Media

    Professor Martin Zacharias

  262. Modulation of SHP‐1 phosphatase activity by monovalent and bivalent SH2 phosphopeptide ligands

    Article • Biopolymers, September 2009, Wiley

    Professor Martin Zacharias

  263. Rationalizing perhydrolase activity of aryl-esterase and subtilisin Carlsberg mutants by molecular dynamics simulations of the second tetrahedral intermediate state

    Article • Theoretical Chemistry Accounts, July 2009, Springer Science + Business Media

    Professor Martin Zacharias

  264. Predicting Affinity and Specificity of Antigenic Peptide Binding to Major Histocompatibility Class I Molecules

    Article • Current Protein and Peptide Science, June 2009, Bentham Science Publishers

    Professor Martin Zacharias

  265. Simulated annealing coupled replica exchange molecular dynamics—An efficient conformational sampling method

    Article • Journal of Structural Biology, June 2009, Elsevier

    Professor Martin Zacharias

  266. PTools: an opensource molecular docking library

    Article • BMC Structural Biology, May 2009, Springer Science + Business Media

    Professor Martin Zacharias

  267. Local and global effects of strong DNA bending induced during molecular dynamics simulations

    Article • Nucleic Acids Research, April 2009, Oxford University Press (OUP)

    Professor Martin Zacharias

  268. Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach

    Article • The Journal of Chemical Physics, March 2009, American Institute of Physics

    Professor Martin Zacharias

  269. Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica—Exchange Molecular Dynamics Simulations

    Article • International Journal of Molecular Sciences, March 2009, MDPI AG

    Professor Martin Zacharias

  270. Folding simulations of Trp‐cage mini protein in explicit solvent using biasing potential replica‐exchange molecular dynamics simulations

    Article • Proteins Structure Function and Bioinformatics, January 2009, Wiley

    Professor Martin Zacharias

  271. Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations

    Article • Physical Chemistry Chemical Physics, January 2009, Royal Society of Chemistry

    Professor Martin Zacharias

  272. Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation study

    Article • Biopolymers, September 2008, Wiley

    Professor Martin Zacharias

  273. Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping

    Article • Journal of Computational Chemistry, August 2008, Wiley

    Professor Martin Zacharias

  274. Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: A molecular dynamics simulation study

    Article • Molecular Immunology, August 2008, Elsevier

    Professor Martin Zacharias

  275. TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism

    Article • Nucleic Acids Research, June 2008, Oxford University Press (OUP)

    Professor Martin Zacharias

  276. How to Efficiently Include Receptor Flexibility During Computational Docking

    Article • Current Computer - Aided Drug Design, June 2008, Bentham Science Publishers

    Professor Martin Zacharias

  277. Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

    Article • Journal of Medicinal Chemistry, June 2008, American Chemical Society (ACS)

    Professor Martin Zacharias

  278. Maturation of the 5S rRNA 5′ end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcanii

    Article • RNA, March 2008, Cold Spring Harbor Laboratory Press

    Professor Martin Zacharias

  279. Dissecting protein–RNA recognition sites

    Article • Nucleic Acids Research, March 2008, Oxford University Press (OUP)

    Professor Martin Zacharias

  280. Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange

    Article • Journal of Chemical Theory and Computation, February 2008, American Chemical Society (ACS)

    Professor Martin Zacharias

  281. Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites

    Article • Nucleic Acids Research, February 2008, Oxford University Press (OUP)

    Professor Martin Zacharias

  282. Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking

    Article • Proteins Structure Function and Bioinformatics, January 2008, Wiley

    Professor Martin Zacharias

  283. The interface of protein-protein complexes: Analysis of contacts and prediction of interactions

    Article • Cellular and Molecular Life Sciences, December 2007, Springer Science + Business Media

    Professor Martin Zacharias

  284. Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations

    Article • Biophysical Journal, November 2007, Elsevier

    Professor Martin Zacharias

  285. Protein–protein docking in CAPRI using ATTRACT to account for global and local flexibility

    Article • Proteins Structure Function and Bioinformatics, October 2007, Wiley

    Professor Martin Zacharias

  286. Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation

    Article • Biopolymers, April 2007, Wiley

    Danilo Roccatano, Professor Martin Zacharias

  287. Temperature Dependence of Looping Rates in a Short Peptide

    Article • The Journal of Physical Chemistry B, March 2007, American Chemical Society (ACS)

    Danilo Roccatano, Professor Martin Zacharias

  288. Comparative molecular dynamics analysis of tapasin‐dependent and ‐independent MHC class I alleles

    Article • Protein Science, February 2007, Wiley

    Professor Martin Zacharias

  289. Enzymatic Degradation ofβ- and Mixedα,β-Oligopeptides

    Article • Chemistry & Biodiversity, December 2006, Wiley

    Dr Michael Limbach, Professor Martin Zacharias

  290. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing‐potential

    Article • Proteins Structure Function and Bioinformatics, November 2006, Wiley

    Professor Martin Zacharias

  291. B-DNA Under Stress: Over- and Untwisting of DNA during Molecular Dynamics Simulations

    Article • Biophysical Journal, October 2006, Elsevier

    Professor Martin Zacharias

  292. Phosphopeptide Ligands of the SHP‐1 N‐SH2 Domain: Effects on Binding and Stimulation of Phosphatase Activity

    Article • ChemMedChem, August 2006, Wiley

    Professor Martin Zacharias

  293. Serum-Stable RNA Aptamers to an Invariant Surface Domain of Live African Trypanosomes

    Article • Combinatorial Chemistry & High Throughput Screening, August 2006, Bentham Science Publishers

    Professor Martin Zacharias

  294. Minor Groove Deformability of DNA: A Molecular Dynamics Free Energy Simulation Study

    Article • Biophysical Journal, August 2006, Elsevier

    Professor Martin Zacharias

  295. Sequence Specificity of SHP-1 and SHP-2 Src Homology 2 Domains

    Article • Journal of Biological Chemistry, July 2006, Elsevier

    Professor Martin Zacharias

  296. Distance Distributions of Short Polypeptides Recovered by Fluorescence Resonance Energy Transfer in the 10 Å Domain

    Article • Journal of the American Chemical Society, June 2006, American Chemical Society (ACS)

    Danilo Roccatano, Professor Martin Zacharias

  297. RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

    Article • Structure, May 2006, Elsevier

    Professor Martin Zacharias

  298. Conformational Transitions in RNA Single Uridine and Adenosine Bulge Structures: A Molecular Dynamics Free Energy Simulation Study

    Article • Biophysical Journal, April 2006, Elsevier

    Professor Martin Zacharias

  299. A Statistical Analysis of Random Mutagenesis Methods Used for Directed Protein Evolution

    Article • Journal of Molecular Biology, January 2006, Elsevier

    Danilo Roccatano, Professor Martin Zacharias

  300. Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: A molecular dynamics simulation study

    Article • Biopolymers, January 2006, Wiley

    Danilo Roccatano, Professor Martin Zacharias

  301. Accounting for loop flexibility during protein–protein docking

    Article • Proteins Structure Function and Bioinformatics, December 2005, Wiley

    Professor Martin Zacharias

  302. Accounting for global protein deformability during protein–protein and protein–ligand docking

    Article • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, December 2005, Elsevier

    Professor Martin Zacharias

  303. Effect of hexafluoroisopropanol alcohol on the structure of melittin: A molecular dynamics simulation study

    Article • Protein Science, October 2005, Wiley

    Danilo Roccatano, Professor Martin Zacharias

  304. Refinement of protein cores and protein–peptide interfaces using a potential scaling approach

    Article • Protein Engineering Design and Selection, September 2005, Oxford University Press (OUP)

    Professor Martin Zacharias

  305. ATTRACT: Protein–protein docking in CAPRI using a reduced protein model

    Article • Proteins Structure Function and Bioinformatics, June 2005, Wiley

    Professor Martin Zacharias

  306. Sensitive Assay for Laboratory Evolution of Hydroxylases toward Aromatic and Heterocyclic Compounds

    Article • April 2005, SAGE Publications

    Danilo Roccatano, Professor Martin Zacharias

  307. Hereditary Lattice Corneal Dystrophy Is Associated with Corneal Amyloid Deposits Enclosing C-Terminal Fragments of Keratoepithelin

    Article • Investigative Ophthalmology & Visual Science, April 2005, Association for Research in Vision and Ophthalmology (ARVO)

    Professor Martin Zacharias

  308. A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA

    Article • Nucleic Acids Research, March 2005, Oxford University Press (OUP)

    Professor Martin Zacharias

  309. Design and Biological Evaluation of Linear and Cyclic Phosphopeptide Ligands of the N-Terminal SH2 Domain of Protein Tyrosine Phosphatase SHP-1

    Article • Journal of Medicinal Chemistry, February 2005, American Chemical Society (ACS)

    Professor Martin Zacharias

  310. Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixture

    Article • Biopolymers, January 2005, Wiley

    Danilo Roccatano, Professor Martin Zacharias

  311. Efficient Search on Energy Minima for Structure Prediction of Nucleic Acid Motifs

    Article • Journal of Biomolecular Structure and Dynamics, December 2004, Taylor & Francis

    Professor Martin Zacharias

  312. Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulations

    Article • Nucleic Acids Research, November 2004, Oxford University Press (OUP)

    Professor Martin Zacharias

  313. Structural and Dynamic Properties of the CAGQW Peptide in Water:  A Molecular Dynamics Simulation Study Using Different Force Fields

    Article • The Journal of Physical Chemistry B, November 2004, American Chemical Society (ACS)

    Danilo Roccatano, Professor Martin Zacharias

  314. Conformational Flexibility of the MHC Class I α1-α2 Domain in Peptide Bound and Free States: A Molecular Dynamics Simulation Study

    Article • Biophysical Journal, October 2004, Elsevier

    Professor Martin Zacharias

  315. The Human T-Cell Lymphotropic Virus Type-I Dimerization Initiation Site Forms a Hairpin Loop, Unlike Previously Characterized Retroviral Dimerization Motifs

    Article • Biochemistry, April 2004, American Chemical Society (ACS)

    Professor Martin Zacharias

  316. Molecular Determinants for High-Affinity Block of Human EAG Potassium Channels by Antiarrhythmic Agents

    Article • Molecular Pharmacology, April 2004, American Society for Pharmacology & Experimental Therapeutics (ASPET)

    Professor Martin Zacharias

  317. Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides

    Article • Journal of Peptide Research, April 2004, Wiley

    Professor Martin Zacharias

  318. Effective Dephosphorylation of Src Substrates by SHP-1

    Article • Journal of Biological Chemistry, March 2004, Elsevier

    Professor Martin Zacharias

  319. Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP

    Article • Proteins Structure Function and Bioinformatics, January 2004, Wiley

    Professor Martin Zacharias

  320. Tapasin and other chaperones: models of the MHC class I loading complex

    Article • Biological Chemistry, January 2004, De Gruyter

    Professor Martin Zacharias

  321. Sequence Context Dependence of Tandem Guanine:Adenine Mismatch Conformations in RNA: A Continuum Solvent Analysis

    Article • Biophysical Journal, July 2003, Elsevier

    Professor Martin Zacharias

  322. Protein–protein docking with a reduced protein model accounting for side‐chain flexibility

    Article • Protein Science, June 2003, Wiley

    Professor Martin Zacharias

  323. Continuum Solvent Modeling of Nonpolar Solvation:  Improvement by Separating Surface Area Dependent Cavity and Dispersion Contributions

    Article • The Journal of Physical Chemistry A, April 2003, American Chemical Society (ACS)

    Professor Martin Zacharias

  324. DAPI binding to the DNA minor groove: a continuum solvent analysis

    Article • Journal of Molecular Recognition, July 2002, Wiley

    Professor Martin Zacharias

  325. Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation

    Article • Nucleic Acids Research, October 2001, Oxford University Press (OUP)

    Professor Martin Zacharias

  326. Conformations of an Adenine Bulge in a DNA Octamer and Its Influence on DNA Structure from Molecular Dynamics Simulations

    Article • Biophysical Journal, July 2001, Elsevier

    Professor Martin Zacharias

  327. Conformational Analysis of DNA-Trinucleotide-Hairpin-Loop Structures Using a Continuum Solvent Model

    Article • Biophysical Journal, May 2001, Elsevier

    Professor Martin Zacharias

  328. Simulation of the structure and dynamics of nonhelical RNA motifs

    Article • Current Opinion in Structural Biology, June 2000, Elsevier

    Professor Martin Zacharias

  329. Conformational Deformability of RNA: A Harmonic Mode Analysis

    Article • Biophysical Journal, May 2000, Elsevier

    Professor Martin Zacharias

  330. Comparison of molecular dynamics and harmonic mode calculations on RNA

    Article • Biopolymers, January 2000, Wiley

    Professor Martin Zacharias

  331. Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model

    Article • Journal of Molecular Biology, June 1999, Elsevier

    Professor Martin Zacharias

  332. Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex

    Article • Journal of Computational Chemistry, February 1999, Wiley

    Professor Martin Zacharias

  333. Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions

    Article • Biophysical Journal, December 1997, Elsevier

    Professor Martin Zacharias

  334. Influence of static and dynamic bends on the birefringence decay profile of RNA helices: Brownian dynamics simulations

    Article • Biophysical Journal, July 1997, Elsevier

    Professor Martin Zacharias

  335. The Influence of Symmetric Internal Loops on the Flexibility of RNA

    Article • Journal of Molecular Biology, March 1996, Elsevier

    Professor Martin Zacharias

  336. The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide.

    Article • Proceedings of the National Academy of Sciences, June 1995, Proceedings of the National Academy of Sciences

    Professor Martin Zacharias

  337. Path Dependence of Free Energy Components in Thermodynamic Integration

    Article • Molecular Simulation, June 1995, Taylor & Francis

    Professor Martin Zacharias

  338. A molecular mechanics/grid method for evaluation of ligand–receptor interactions

    Article • Journal of Computational Chemistry, April 1995, Wiley

    Professor Martin Zacharias

  339. Bulge-Induced Bends in RNA: Quantification by Transient Electric Birefringence

    Article • Journal of Molecular Biology, March 1995, Elsevier

    Professor Martin Zacharias

  340. Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration

    Article • The Journal of Chemical Physics, June 1994, American Institute of Physics

    Professor Martin Zacharias

  341. Combined Conformational Search and Finite-Difference Poisson?Boltzmann Approach for Flexible Docking

    Article • Journal of Molecular Biology, May 1994, Elsevier

    Professor Martin Zacharias

  342. Inversion of receptor binding preferences by mutagenesis: Free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins

    Article • Biochemistry, July 1993, American Chemical Society (ACS)

    Professor Martin Zacharias

  343. Poisson-Boltzmann analysis of the lambda repressor-operator interaction

    Article • Biophysical Journal, November 1992, Elsevier

    Professor Martin Zacharias

  344. Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations

    Article • Chemical Physics Letters, August 1992, Elsevier

    Professor Martin Zacharias

  345. Analysis of the Fis-dependent and Fis-independent transcription activation mechanisms of the Escherichia coli ribosomal RNA P1 promoter

    Article • Biochemistry, March 1992, American Chemical Society (ACS)

    Professor Martin Zacharias

  346. Analysis of sequence elements important for the synthesis and control of ribosomal RNA in E coli

    Article • Biochimie, June 1991, Elsevier

    Professor Martin Zacharias

  347. Polyacrylamide gradient gel electrophoresis for the detection of bended DNA fragments

    Article • Nucleic Acids Research, January 1990, Oxford University Press (OUP)

    Professor Martin Zacharias

  348. The signal for growth rate control and stringent sensitivity inE. coliis not restricted to a particular sequence motif within the promoter region

    Article • Nucleic Acids Research, January 1990, Oxford University Press (OUP)

    Professor Martin Zacharias

  349. The tLstructure within the leader region ofEscherichia coliribosomal RNA operons has post-transcriptional functions

    Article • Nucleic Acids Research, January 1990, Oxford University Press (OUP)

    Professor Martin Zacharias

  350. Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2- and tac promoter on growth-rate control and stringent sensitivity.

    Article • The EMBO Journal, November 1989, Springer Science + Business Media

    Professor Martin Zacharias

  351. Functional characterization of a putative internal promoter sequence between the 16S and the 23S RNA genes within the Escherichia coli rrnB operon

    Article • Molecular Microbiology, March 1989, Wiley

    Professor Martin Zacharias

  352. Deletions in the tLstructure upstream to the rRNA genes in theE.colirmB operon cause transcription polarity

    Article • Nucleic Acids Research, January 1987, Oxford University Press (OUP)

    Professor Martin Zacharias

  353. The importance of individual nucleotides for the structure and function of rRNA molecules in E. coli

    Article • FEBS Letters, August 1986, Wiley

    Professor Martin Zacharias

  354. Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands

    Article • Springer Science + Business Media

    Professor Martin Zacharias

  355. RNA Aptamers as Potential Pharmaceuticals Against Infections with African Trypanosomes

    Article • Springer Science + Business Media

    Professor Martin Zacharias