All Stories

  1. Optogenetically engineered Septin-7 enhances immune cell infiltration of tumor spheroids

    Article • Proceedings of the National Academy of Sciences, October 2024, Proceedings of the National Academy of Sciences

    Professor Nikolay V Dokholyan

  2. Faculty Opinions recommendation of Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells.

    Article • July 2014, F1000Research

    Professor Nikolay V Dokholyan

  3. Pore Dynamics and Conductance of RyR1 Transmembrane Domain

    Article • Biophysical Journal, June 2014, Elsevier

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  4. Intrinsic Disorder Mediates Cooperative Signal Transduction in STIM1

    Article • Journal of Molecular Biology, May 2014, Elsevier

    Professor Nikolay V Dokholyan

  5. Identification of an Actin Binding Surface on Vinculin that Mediates Mechanical Cell and Focal Adhesion Properties

    Article • Structure, May 2014, Elsevier

    Professor Nikolay V Dokholyan

  6. Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

    Article • PLoS ONE, April 2014, PLOS

    Professor Nikolay V Dokholyan

  7. Faculty Opinions recommendation of Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype.

    Article • April 2014, F1000Research

    Professor Nikolay V Dokholyan

  8. Non-native Soluble Oligomers of Cu/Zn Superoxide Dismutase (SOD1) Contain a Conformational Epitope Linked to Cytotoxicity in Amyotrophic Lateral Sclerosis (ALS)

    Article • Biochemistry, April 2014, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  9. Faculty Opinions recommendation of Alzheimer's - Looking beyond plaques.

    Article • February 2014, F1000Research

    Professor Nikolay V Dokholyan

  10. Faculty Opinions recommendation of Kynurenine 3-monooxygenase inhibition in blood ameliorates neurodegeneration.

    Article • December 2013, F1000Research

    Professor Nikolay V Dokholyan

  11. The maturation of HIV‐1 protease precursor studied by discrete molecular dynamics

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

    Professor Nikolay V Dokholyan

  12. Faculty Opinions recommendation of Deamidation of asparagine to aspartate destabilizes Cu, Zn superoxide dismutase, accelerates fibrillization, and mirrors ALS-linked mutations.

    Article • October 2013, F1000Research

    Professor Nikolay V Dokholyan

  13. Faculty Opinions recommendation of Integrative genomics identifies APOE ε4 effectors in Alzheimer's disease.

    Article • October 2013, F1000Research

    Professor Nikolay V Dokholyan

  14. Faculty Opinions recommendation of Small-molecule conversion of toxic oligomers to nontoxic β-sheet-rich amyloid fibrils.

    Article • September 2013, F1000Research

    Professor Nikolay V Dokholyan

  15. Identification of Novel Integrin Binding Partners for Calcium and Integrin Binding Protein 1 (CIB1): Structural and Thermodynamic Basis of CIB1 Promiscuity

    Article • Biochemistry, September 2013, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  16. Faculty Opinions recommendation of Pathological α-synuclein transmission initiates Parkinson-like neurodegeneration in nontransgenic mice.

    Article • August 2013, F1000Research

    Professor Nikolay V Dokholyan

  17. Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches

    Article • Journal of Chemical Information and Modeling, July 2013, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  18. Protein HP1028 from the human pathogenHelicobacter pyloribelongs to the lipocalin family

    Article • Acta Crystallographica Section D Biological Crystallography, July 2013, International Union of Crystallography

    Professor Nikolay V Dokholyan

  19. RNA Junction Motifs as Scaffolds for Construction of Multifunctional RNA Nanoparticles

    Article • July 2013, Taylor & Francis

    Professor Nikolay V Dokholyan

  20. Knowledge-Based Design of a Biosensor to Quantify Localized ERK Activation in Living Cells

    Article • Chemistry & Biology, June 2013, Elsevier

    Professor Nikolay V Dokholyan

  21. Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics

    Article • Biophysical Journal, June 2013, Elsevier

    Professor Nikolay V Dokholyan

  22. Faculty Opinions recommendation of Selective protein synthesis by ribosomes with a drug-obstructed exit tunnel.

    Article • April 2013, F1000Research

    Professor Nikolay V Dokholyan

  23. Correction: Thermal Unfolding Pathway of PHD2 Catalytic Domain in Three Different PHD2 Species: Computational Approaches

    Article • PLoS ONE, April 2013, PLOS

    Professor Nikolay V Dokholyan

  24. Faculty Opinions recommendation of Probing allostery through DNA.

    Article • April 2013, F1000Research

    Professor Nikolay V Dokholyan

  25. Faculty Opinions recommendation of Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies.

    Article • March 2013, F1000Research

    Professor Nikolay V Dokholyan

  26. Highly covarying residues have a functional role in antibody constant domains

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

    Professor Nikolay V Dokholyan

  27. Metric to Distinguish Closely Related Domain Families Using Sequence Information

    Article • Journal of Molecular Biology, February 2013, Elsevier

    Professor Nikolay V Dokholyan, Professor Nikolay V Dokholyan

  28. Faculty Opinions recommendation of Inducible, reversible system for the rapid and complete degradation of proteins in mammalian cells.

    Article • January 2013, F1000Research

    Professor Nikolay V Dokholyan

  29. From Disordered Amyloid β-Proteins to Soluble Oligomers and Protofibrils Using Discrete Molecular Dynamics

    Article • January 2013, World Scientific Pub Co Pte Lt

    Professor Nikolay V Dokholyan, Professor Brigita Urbanc

  30. Statistical Analysis of SHAPE-Directed RNA Secondary Structure Modeling

    Article • Biochemistry, January 2013, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  31. Principles for Understanding the Accuracy of SHAPE-Directed RNA Structure Modeling

    Article • Biochemistry, January 2013, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  32. Is Protein Destabilization a Widespread Factor in Genetic Disease?

    Article • Biophysical Journal, January 2013, Elsevier

    Professor Nikolay V Dokholyan

  33. Generation of a Light Inhibited Src Kinase through Insertion of LOV into the Catalytic Domain

    Article • Biophysical Journal, January 2013, Elsevier

    Professor Nikolay V Dokholyan

  34. Rational Design of a Ligand-Controlled Protein Conformational Switch

    Article • Biophysical Journal, January 2013, Elsevier

    Professor Nikolay V Dokholyan

  35. Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark

    Article • Journal of Chemical Information and Modeling, December 2012, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  36. Faculty Opinions recommendation of Role of pro-brain-derived neurotrophic factor (proBDNF) to mature BDNF conversion in activity-dependent competition at developing neuromuscular synapses.

    Article • December 2012, F1000Research

    Professor Nikolay V Dokholyan

  37. Faculty Opinions recommendation of Crystal structure of the calcium release-activated calcium channel Orai.

    Article • December 2012, F1000Research

    Professor Nikolay V Dokholyan

  38. Faculty Opinions recommendation of Rational design of potent domain antibody inhibitors of amyloid fibril assembly.

    Article • December 2012, F1000Research

    Professor Nikolay V Dokholyan

  39. New Models of Tetrahymena Telomerase RNA from Experimentally Derived Constraints and Modeling

    Article • Journal of the American Chemical Society, December 2012, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  40. Faculty Opinions recommendation of MYC suppresses cancer metastasis by direct transcriptional silencing of αv and β3 integrin subunits.

    Article • November 2012, F1000Research

    Professor Nikolay V Dokholyan

  41. Faculty Opinions recommendation of Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography.

    Article • November 2012, F1000Research

    Professor Nikolay V Dokholyan

  42. Faculty Opinions recommendation of Structure of an intermediate state in protein folding and aggregation.

    Article • November 2012, F1000Research

    Professor Nikolay V Dokholyan

  43. Faculty Opinions recommendation of Principles for designing ideal protein structures.

    Article • November 2012, F1000Research

    Professor Nikolay V Dokholyan

  44. Faculty Opinions recommendation of Modulation of voltage-gated K+ channels by the sodium channel β1 subunit.

    Article • November 2012, F1000Research

    Professor Nikolay V Dokholyan

  45. Thermal Unfolding Pathway of PHD2 Catalytic Domain in Three Different PHD2 Species: Computational Approaches

    Article • PLoS ONE, October 2012, PLOS

    Professor Nikolay V Dokholyan

  46. Faculty Opinions recommendation of Monitoring spatiotemporal biogenesis of macromolecular assemblies by pulse-chase epitope labeling.

    Article • October 2012, F1000Research

    Professor Nikolay V Dokholyan

  47. Recognition of Platinum–DNA Adducts by HMGB1a

    Article • Biochemistry, September 2012, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  48. ChemInform Abstract: Discrete Molecular Dynamics

    Article • ChemInform, September 2012, Wiley

    Professor Nikolay V Dokholyan

  49. Hybrid Dynamics Simulation Engine for Metalloproteins

    Article • Biophysical Journal, August 2012, Elsevier

    Professor Nikolay V Dokholyan

  50. Local Unfolding of Cu, Zn Superoxide Dismutase Monomer Determines the Morphology of Fibrillar Aggregates

    Article • Journal of Molecular Biology, August 2012, Elsevier

    Professor Nikolay V Dokholyan

  51. Harnessing a Physiologic Mechanism for siRNA Delivery With Mimetic Lipoprotein Particles

    Article • Molecular Therapy, August 2012, Elsevier

    Professor Nikolay V Dokholyan

  52. Faculty Opinions recommendation of Interaction of cisplatin with human superoxide dismutase.

    Article • July 2012, F1000Research

    Professor Nikolay V Dokholyan

  53. Faculty Opinions recommendation of Three-dimensional reconstruction of protein networks provides insight into human genetic disease.

    Article • July 2012, F1000Research

    Professor Nikolay V Dokholyan

  54. Faculty Opinions recommendation of Dynamics and memory of heterochromatin in living cells.

    Article • June 2012, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  55. Faculty Opinions recommendation of Early steps in oxidation-induced SOD1 misfolding: implications for non-amyloid protein aggregation in familial ALS.

    Article • June 2012, F1000Research

    Professor Nikolay V Dokholyan

  56. Faculty Opinions recommendation of Genetic switchboard for synthetic biology applications.

    Article • May 2012, F1000Research

    Professor Nikolay V Dokholyan

  57. Corrigendum to “ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions” [Biochim. Biophys. Acta 1808 (2011) 2954–2964]

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, May 2012, Elsevier

    Professor Nikolay V Dokholyan

  58. Allosteric Modulation Balances Thermodynamic Stability and Restores Function of ΔF508 CFTR

    Article • Journal of Molecular Biology, May 2012, Elsevier

    Professor Nikolay V Dokholyan

  59. The interface of protein structure, protein biophysics, and molecular evolution

    Article • Protein Science, April 2012, Wiley

    Professor Nikolay V Dokholyan

  60. Three-dimensional RNA structure refinement by hydroxyl radical probing

    Article • Nature Chemical Biology, April 2012, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  61. Energetic and Structural Basis for Activation of the Epithelial Sodium Channel by Matriptase

    Article • Biochemistry, April 2012, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  62. Faculty Opinions recommendation of Tracking protein aggregation and mislocalization in cells with flow cytometry.

    Article • March 2012, F1000Research

    Professor Nikolay V Dokholyan

  63. Faculty Opinions recommendation of Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops.

    Article • March 2012, F1000Research

    Professor Nikolay V Dokholyan

  64. Faculty Opinions recommendation of An over-oxidized form of superoxide dismutase found in sporadic amyotrophic lateral sclerosis with bulbar onset shares a toxic mechanism with mutant SOD1.

    Article • March 2012, F1000Research

    Professor Nikolay V Dokholyan

  65. Physical Microscopic Model of Proteins Under Force

    Article • The Journal of Physical Chemistry B, March 2012, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  66. Faculty Opinions recommendation of Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

    Article • March 2012, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  67. Intra- and Inter-Subunit Disulfide Bond Formation Is Nonessential in Adeno-Associated Viral Capsids

    Article • PLoS ONE, February 2012, PLOS

    Professor Nikolay V Dokholyan

  68. Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

    Article • The Journal of Physical Chemistry B, February 2012, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  69. Computational Modeling of Biological Systems

    Article • January 2012

    Professor Nikolay V Dokholyan

  70. Computational Modeling of Telomerase in Action

    Article • Biophysical Journal, January 2012, Elsevier

    Professor Nikolay V Dokholyan

  71. Discrete Molecular Dynamics Simulation of Biomolecules

    Article • January 2012, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  72. Multiscale Modeling of RNA Structure and Dynamics

    Article • January 2012, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  73. Discrete Molecular Dynamics Distinguishes Nativelike Binding Poses from Decoys in Difficult Targets

    Article • Biophysical Journal, January 2012, Elsevier

    Professor Nikolay V Dokholyan

  74. The Complex Molecular Biology of Amyotrophic Lateral Sclerosis (ALS)

    Article • January 2012, Elsevier

    Professor Nikolay V Dokholyan

  75. Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism

    Article • January 2012, Springer Science + Business Media

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  76. Serotonin-Induced Hypersensitivity via Inhibition of Catechol O-Methyltransferase Activity

    Article • Molecular Pain, January 2012, SAGE Publications

    Professor Nikolay V Dokholyan

  77. Faculty Opinions recommendation of Aspartate 112 is the selectivity filter of the human voltage-gated proton channel.

    Article • December 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  78. Faculty Opinions recommendation of Mapping intact protein isoforms in discovery mode using top-down proteomics.

    Article • December 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  79. Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening

    Article • Journal of Chemical Information and Modeling, December 2011, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  80. Structural and Dynamic Determinants of Protein-Peptide Recognition

    Article • Structure, December 2011, Elsevier

    Professor Nikolay V Dokholyan

  81. ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, December 2011, Elsevier

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  82. Structural Basis for μ-Opioid Receptor Binding and Activation

    Article • Structure, November 2011, Elsevier

    Professor Nikolay V Dokholyan

  83. Faculty Opinions recommendation of α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation.

    Article • September 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  84. Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations

    Article • PLoS Computational Biology, September 2011, PLOS

    Professor Nikolay V Dokholyan

  85. Structural Mechanism of S-Adenosyl Methionine Binding to Catechol O-Methyltransferase

    Article • PLoS ONE, August 2011, PLOS

    Professor Nikolay V Dokholyan

  86. Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets

    Article • Journal of Chemical Information and Modeling, August 2011, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  87. Flanking Bases Influence the Nature of DNA Distortion by Platinum 1,2-Intrastrand (GG) Cross-Links

    Article • PLoS ONE, August 2011, PLOS

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  88. Faculty Opinions recommendation of The crystal structure of a voltage-gated sodium channel.

    Article • July 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  89. Glutathionylation at Cys-111 Induces Dissociation of Wild Type and FALS Mutant SOD1 Dimers

    Article • Biochemistry, July 2011, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  90. A Physical Model Reveals the Mechanochemistry Responsible for Dynein's Processive Motion

    Article • Biophysical Journal, July 2011, Elsevier

    Professor Nikolay V Dokholyan

  91. Faculty Opinions recommendation of Phosphorylation-dependent kinase-substrate cross-linking.

    Article • June 2011, F1000Research

    Professor Nikolay V Dokholyan

  92. Faculty Opinions recommendation of Structure of an agonist-bound human A2A adenosine receptor.

    Article • May 2011, F1000Research

    Professor Nikolay V Dokholyan

  93. Faculty Opinions recommendation of Critical nucleus size for disease-related polyglutamine aggregation is repeat-length dependent.

    Article • May 2011, F1000Research

    Professor Nikolay V Dokholyan

  94. Towards quantitative biochemistry: research and reports in biochemistry

    Article • Research and Reports in Biochemistry, May 2011, Taylor & Francis

    Professor Nikolay V Dokholyan

  95. Structural and Thermodynamic Effects of Post-translational Modifications in Mutant and Wild Type Cu, Zn Superoxide Dismutase

    Article • Journal of Molecular Biology, May 2011, Elsevier

    Professor Nikolay V Dokholyan

  96. Regioselectivity of catechol O-methyltransferase confers enhancement of catalytic activity

    Article • Chemical Physics Letters, April 2011, Elsevier

    Professor Nikolay V Dokholyan

  97. Rigid substructure search

    Article • Bioinformatics, April 2011, Oxford University Press (OUP)

    Professor Nikolay V Dokholyan

  98. Approaches for probing the sequence space of substrates recognized by molecular chaperones

    Article • Methods, March 2011, Elsevier

    Professor Nikolay V Dokholyan

  99. A Folding Pathway-Dependent Score to Recognize Membrane Proteins

    Article • PLoS ONE, March 2011, PLOS

    Professor Nikolay V Dokholyan

  100. Faculty Opinions recommendation of Structure of a nanobody-stabilized active state of the β(2) adrenoceptor.

    Article • February 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  101. Engineered Allosteric Activation of Kinases in Living Cells

    Article • Biophysical Journal, February 2011, Elsevier

    Professor Nikolay V Dokholyan

  102. Thermodynamic Stability of Histone H3 is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

    Article • Biophysical Journal, February 2011, Elsevier

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  103. Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA

    Article • PLoS Computational Biology, January 2011, PLOS

    Professor Nikolay V Dokholyan

  104. Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

    Article • PLoS Computational Biology, January 2011, PLOS

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  105. Fingerprint‐based structure retrieval using electron density

    Article • Proteins Structure Function and Bioinformatics, January 2011, Wiley

    Professor Nikolay V Dokholyan

  106. Discrete molecular dynamics

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, January 2011, Wiley

    Professor Nikolay V Dokholyan

  107. Molecular Modeling Tools and Approaches for CFTR and Cystic Fibrosis

    Article • January 2011, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  108. Light Regulation of Protein Dimerization and Kinase Activity in Living Cells Using Photocaged Rapamycin and Engineered FKBP

    Article • Journal of the American Chemical Society, December 2010, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  109. Faculty Opinions recommendation of Alleviating cancer drug toxicity by inhibiting a bacterial enzyme.

    Article • November 2010, F1000Research

    Professor Nikolay V Dokholyan

  110. Automated minimization of steric clashes in protein structures

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

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  111. Faculty Opinions recommendation of Single-molecule derivation of salt dependent base-pair free energies in DNA.

    Article • October 2010, F1000Research

    Professor Nikolay V Dokholyan

  112. Faculty Opinions recommendation of Charges in the hydrophobic interior of proteins.

    Article • September 2010, F1000Research

    Professor Nikolay V Dokholyan

  113. Faculty Opinions recommendation of iAlign: a method for the structural comparison of protein-protein interfaces.

    Article • September 2010, F1000Research

    Professor Nikolay V Dokholyan

  114. Faculty Opinions recommendation of Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T.

    Article • September 2010, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  115. Modeling Mutations in Proteins Using Medusa and Discrete Molecule Dynamics

    Article • September 2010, Wiley

    Professor Nikolay V Dokholyan

  116. Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands

    Article • Journal of Chemical Information and Modeling, August 2010, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  117. A Didactic Model of Macromolecular Crowding Effects on Protein Folding

    Article • PLoS ONE, August 2010, PLOS

    Professor Nikolay V Dokholyan

  118. Faculty Opinions recommendation of Single-molecule pulling simulations can discern active from inactive enzyme inhibitors.

    Article • August 2010, F1000Research

    Professor Nikolay V Dokholyan

  119. Regulatory Insertion Removal Restores Maturation, Stability and Function of ΔF508 CFTR

    Article • Journal of Molecular Biology, August 2010, Elsevier

    Professor Nikolay V Dokholyan

  120. Faculty Opinions recommendation of A distinctive role for focal adhesion proteins in three-dimensional cell motility.

    Article • July 2010, F1000Research

    Professor Nikolay V Dokholyan

  121. Computational Design of a PAK1 Binding Protein

    Article • Journal of Molecular Biology, July 2010, Elsevier

    Professor Nikolay V Dokholyan

  122. Engineered allosteric activation of kinases in living cells

    Article • Nature Biotechnology, June 2010, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  123. Correction to Robust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain

    Article • Biochemistry, June 2010, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  124. Faculty Opinions recommendation of Protein interface conservation across structure space.

    Article • June 2010, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  125. Faculty Opinions recommendation of A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps.

    Article • June 2010, F1000Research

    Professor Nikolay V Dokholyan

  126. Faculty Opinions recommendation of Structure-based design of a photocontrolled DNA binding protein.

    Article • May 2010, F1000Research

    Professor Nikolay V Dokholyan

  127. Robust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain

    Article • Biochemistry, May 2010, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  128. Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences

    Article • PLoS Computational Biology, April 2010, PLOS

    Professor Nikolay V Dokholyan

  129. Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases

    Article • Pflügers Archiv - European Journal of Physiology, April 2010, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  130. Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity

    Article • Physical Chemistry Chemical Physics, January 2010, Royal Society of Chemistry

    Professor Nikolay V Dokholyan

  131. Multiscale Modeling and Design of Molecular Conformational States

    Article • Biophysical Journal, January 2010, Elsevier

    Professor Nikolay V Dokholyan

  132. Computational Evaluation of Protein Stability Change upon Mutations

    Article • January 2010, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  133. A Coupling of Structural and Kinetic Models Reveals the Stepping Mechanics of Dynein

    Article • Biophysical Journal, January 2010, Elsevier

    Professor Nikolay V Dokholyan

  134. Identification of a Consensus Motif in Substrates Bound by a Type I Hsp40

    Article • Biophysical Journal, January 2010, Elsevier

    Professor Nikolay V Dokholyan

  135. N‐terminal strands of filamin Ig domains act as a conformational switch under biological forces

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

    Professor Nikolay V Dokholyan

  136. Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

    Article • PLoS Computational Biology, July 2009, PLOS

    Professor Nikolay V Dokholyan

  137. A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)

    Article • PLoS Computational Biology, April 2009, PLOS

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  138. Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics

    Article • Journal of the American Chemical Society, February 2009, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  139. Ryanodine Receptor Pore Structure and Function

    Article • Biophysical Journal, February 2009, Elsevier

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  140. Phenylalanine 508 Forms Intra-domain Contact Crucial To CFTR Folding And Dynamics

    Article • Biophysical Journal, February 2009, Elsevier

    Professor Nikolay V Dokholyan

  141. Outcome of a Workshop on Applications of Protein Models in Biomedical Research

    Article • Structure, February 2009, Elsevier

    Professor Nikolay V Dokholyan

  142. Kinetic models for the coordinated stepping of cytoplasmic dynein

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

    Professor Nikolay V Dokholyan

  143. Multiscale approaches for studying energy transduction in dynein

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

    Professor Nikolay V Dokholyan

  144. Differences in Conformation and Conformational Dynamics Between Cisplatin and Oxaliplatin DNA Adducts

    Article • January 2009, Springer Science + Business Media

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  145. ChemInform Abstract: MedusaScore: An Accurate Force Field‐Based Scoring Function for Virtual Drug Screening.

    Article • ChemInform, November 2008, Wiley

    Professor Nikolay V Dokholyan

  146. MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

    Article • Journal of Chemical Information and Modeling, August 2008, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan, Dr Lada Biedermannová

  147. Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers

    Article • PLoS Computational Biology, August 2008, PLOS

    Professor Nikolay V Dokholyan

  148. Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions

    Article • PLoS Computational Biology, July 2008, PLOS

    Professor Nikolay V Dokholyan

  149. Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels

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

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  150. Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

    Article • Structure, July 2008, Elsevier

    Professor Nikolay V Dokholyan

  151. Computational Studies Reveal Phosphorylation-dependent Changes in the Unstructured R Domain of CFTR

    Article • Journal of Molecular Biology, May 2008, Elsevier

    Professor Nikolay V Dokholyan

  152. Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding

    Article • PLoS Computational Biology, February 2008, PLOS

    Professor Nikolay V Dokholyan

  153. DNA Sequence Mediates Nucleosome Structure and Stability

    Article • Biophysical Journal, January 2008, Elsevier

    Professor Nikolay V Dokholyan

  154. Protein folding: Then and now

    Article • Archives of Biochemistry and Biophysics, January 2008, Elsevier

    Professor Nikolay V Dokholyan

  155. Modeling Backbone Flexibility Improves Protein Stability Estimation

    Article • Structure, December 2007, Elsevier

    Professor Nikolay V Dokholyan

  156. Molecular Mechanisms of Polypeptide Aggregation in Human Diseases

    Article • Current Protein and Peptide Science, December 2007, Bentham Science Publishers

    Professor Nikolay V Dokholyan

  157. Molecular Dynamic Simulations of Cisplatin- and Oxaliplatin-d(GG) Intrastand Cross-links Reveal Differences in their Conformational Dynamics

    Article • Journal of Molecular Biology, November 2007, Elsevier

    Professor Nikolay V Dokholyan

  158. Deciphering Protein Dynamics from NMR Data Using Explicit Structure Sampling and Selection

    Article • Biophysical Journal, October 2007, Elsevier

    Professor Nikolay V Dokholyan

  159. Eris: an automated estimator of protein stability

    Article • Nature Chemical Biology, June 2007, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  160. Fidelity of the Protein Structure Reconstruction from Inter-Residue Proximity Constraints

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

    Professor Nikolay V Dokholyan

  161. Insights into thermophilic archaebacterial membrane stability from simplified models of lipid membranes

    Article • Physical Review E, May 2007, American Physical Society (APS)

    Professor Nikolay V Dokholyan

  162. Multiscale Modeling of Nucleosome Dynamics

    Article • Biophysical Journal, March 2007, Elsevier

    Professor Nikolay V Dokholyan

  163. Towards Unifying Protein Evolution Theory

    Article • January 2007, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  164. Similarity and dissimilarity in correlations of genomic DNA

    Article • Physica A Statistical Mechanics and its Applications, January 2007, Elsevier

    Professor Nikolay V Dokholyan

  165. Combining Fluorescence Detection and Mass Spectrometric Analysis for Comprehensive and Quantitative Analysis of Redox-Sensitive Cysteines in Native Membrane Proteins

    Article • Analytical Chemistry, October 2006, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan

  166. The coordinated evolution of yeast proteins is constrained by functional modularity

    Article • Trends in Genetics, August 2006, Elsevier

    Professor Nikolay V Dokholyan

  167. Emergence of Protein Fold Families through Rational Design

    Article • PLoS Computational Biology, July 2006, PLOS

    Professor Nikolay V Dokholyan

  168. The path of DNA in the kinetochore

    Article • Current Biology, April 2006, Elsevier

    Professor Nikolay V Dokholyan

  169. Topological Determinants of Protein Domain Swapping

    Article • Structure, January 2006, Elsevier

    Professor Nikolay V Dokholyan

  170. Correction: Emergence of Protein Fold Families through Rational Design

    Article • PLoS Computational Biology, January 2006, PLOS

    Professor Nikolay V Dokholyan

  171. FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: A large-scale thermodynamic analysis

    Article • Amyloid, January 2006, Taylor & Francis

    Professor Nikolay V Dokholyan

  172. A Single Disulfide Bond Differentiates Aggregation Pathways of ß2-Microglobulin

    Article • Journal of Molecular Biology, November 2005, Elsevier

    Professor Nikolay V Dokholyan

  173. Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation

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

    Professor Nikolay V Dokholyan

  174. Simple but predictive protein models

    Article • Trends in Biotechnology, September 2005, Elsevier

    Professor Nikolay V Dokholyan

  175. Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases

    Article • PLoS Computational Biology, August 2005, PLOS

    Professor Nikolay V Dokholyan

  176. Reconstruction of the src-SH3 Protein Domain Transition State Ensemble using Multiscale Molecular Dynamics Simulations

    Article • Journal of Molecular Biology, July 2005, Elsevier

    Professor Nikolay V Dokholyan

  177. The architecture of the protein domain universe

    Article • Gene, March 2005, Elsevier

    Professor Nikolay V Dokholyan

  178. Emergence of protein fold families through rational design

    Article • PLoS Computational Biology, January 2005, PLOS

    Professor Nikolay V Dokholyan

  179. Molecular origin of polyglutamine aggregation in neurodegenerative diseases

    Article • PLoS Computational Biology, January 2005, PLOS

    Professor Nikolay V Dokholyan

  180. Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model

    Article • Biophysical Journal, January 2005, Elsevier

    Professor Nikolay V Dokholyan

  181. New Insights into FAK Signaling and Localization Based on Detection of a FAT Domain Folding Intermediate

    Article • Structure, December 2004, Elsevier

    Professor Nikolay V Dokholyan

  182. The evolution dynamics of model proteins

    Article • The Journal of Chemical Physics, August 2004, American Institute of Physics

    Professor Nikolay V Dokholyan

  183. Multiple Folding Pathways of the SH3 Domain

    Article • Biophysical Journal, July 2004, Elsevier

    Professor Nikolay V Dokholyan

  184. Can Contact Potentials Reliably Predict Stability of Proteins?

    Article • Journal of Molecular Biology, March 2004, Elsevier

    Professor Nikolay V Dokholyan

  185. What is the protein design alphabet?

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

    Professor Nikolay V Dokholyan

  186. Protein Evolution within a Structural Space

    Article • Biophysical Journal, November 2003, Elsevier

    Professor Nikolay V Dokholyan

  187. Folding of Cu, Zn Superoxide Dismutase and Familial Amyotrophic Lateral Sclerosis

    Article • Journal of Molecular Biology, November 2003, Elsevier

    Professor Nikolay V Dokholyan

  188. Possible Mechanism for Cold Denaturation of Proteins at High Pressure

    Article • Physical Review Letters, September 2003, American Physical Society (APS)

    Professor Nikolay V Dokholyan

  189. Mechanism for the α‐helix to β‐hairpin transition

    Article • Proteins Structure Function and Bioinformatics, September 2003, Wiley

    Professor Nikolay V Dokholyan

  190. Postbreakthrough behavior in flow through porous media

    Article • May 2003, American Physical Society (APS)

    Professor Nikolay V Dokholyan

  191. Functional Fingerprints of Folds: Evidence for Correlated Structure–Function Evolution

    Article • Journal of Molecular Biology, February 2003, Elsevier

    Professor Nikolay V Dokholyan

  192. Identifying Importance of Amino Acids for Protein Folding from Crystal Structures

    Article • January 2003, Elsevier

    Professor Nikolay V Dokholyan

  193. Molecular Dynamics Simulation of the SH3 Domain Aggregation Suggests a Generic Amyloidogenesis Mechanism

    Article • Journal of Molecular Biology, December 2002, Elsevier

    Professor Nikolay V Dokholyan

  194. Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble

    Article • Biophysical Journal, December 2002, Elsevier

    Professor Nikolay V Dokholyan

  195. Understanding conserved amino acids in proteins

    Article • Physica A Statistical Mechanics and its Applications, November 2002, Elsevier

    Professor Nikolay V Dokholyan

  196. Thermodynamics and Folding Kinetics Analysis of the SH3 Domain form Discrete Molecular Dynamics

    Article • Journal of Molecular Biology, May 2002, Elsevier

    Professor Nikolay V Dokholyan

  197. Glassy behavior of a homopolymer from molecular dynamics simulations

    Article • February 2002, American Physical Society (APS)

    Professor Nikolay V Dokholyan

  198. Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

    Article • Journal of Molecular Biology, September 2001, Elsevier

    Professor Nikolay V Dokholyan

  199. Thermodynamically important contacts in folding of model proteins

    Article • February 2001, American Physical Society (APS)

    Professor Nikolay V Dokholyan, Dr Antonio Scala

  200. Flow between two sites on a percolation cluster

    Article • December 2000, American Physical Society (APS)

    Professor Nikolay V Dokholyan

  201. Dependence of conductance on percolation backbone mass

    Article • April 2000, American Physical Society (APS)

    Professor Nikolay V Dokholyan

  202. Identifying the protein folding nucleus using molecular dynamics

    Article • Journal of Molecular Biology, March 2000, Elsevier

    Professor Nikolay V Dokholyan

  203. Distributions of Dimeric Tandem Repeats in Non-coding and Coding DNA Sequences

    Article • Journal of Theoretical Biology, February 2000, Elsevier

    Professor Nikolay V Dokholyan

  204. Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences

    Article • Physica A Statistical Mechanics and its Applications, November 1999, Elsevier

    Professor Nikolay V Dokholyan

  205. Traveling time and traveling length in critical percolation clusters

    Article • September 1999, American Physical Society (APS)

    Professor Nikolay V Dokholyan

  206. Distribution of shortest paths in percolation

    Article • Physica A Statistical Mechanics and its Applications, April 1999, Elsevier

    Professor Nikolay V Dokholyan

  207. Predicting oil recovery using percolation

    Article • Physica A Statistical Mechanics and its Applications, April 1999, Elsevier

    Professor Nikolay V Dokholyan

  208. Scaling of the Distribution of Shortest Paths in Percolation

    Article • Journal of Statistical Physics, November 1998, Springer Science + Business Media

    Professor Nikolay V Dokholyan

  209. Discrete molecular dynamics studies of the folding of a protein-like model

    Article • Folding and Design, November 1998, Elsevier

    Professor Nikolay V Dokholyan

  210. Model of unequal chromosomal crossing over in DNA sequences

    Article • Physica A Statistical Mechanics and its Applications, January 1998, Elsevier

    Professor Nikolay V Dokholyan

  211. Distribution of Base Pair Repeats in Coding and Noncoding DNA Sequences

    Article • Physical Review Letters, December 1997, American Physical Society (APS)

    Professor Nikolay V Dokholyan

  212. Scale-Free Evolution

    Article • Springer Science + Business Media

    Professor Nikolay V Dokholyan