All Stories

  1. MDZip: Neural Compression of Molecular Dynamics Trajectories for Scalable Storage and Ensemble Reconstruction

    Article • The Journal of Physical Chemistry, October 2025, American Chemical Society (ACS)

    Dr Alberto Perez

  2. ATP allosterically regulates an acyl-CoA oxidase

    Article • Nature Communications, August 2025, Springer Science + Business Media

    Dr Alberto Perez

  3. How Well Do Molecular Dynamics Force Fields Model Peptides? A Systematic Benchmark Across Diverse Folding Behaviors

    Article • August 2025, Cold Spring Harbor Laboratory Press

    Dr Alberto Perez

  4. Predicting rare DNA conformations via dynamical graphical models: a case study of the B→A transition

    Article • Nucleic Acids Research, July 2025, Oxford University Press (OUP)

    Dr Alberto Perez

  5. Hierarchical Extended Linkage Method (HELM)’s Deep Dive into Hybrid Clustering Strategies

    Article • Journal of Chemical Information and Modeling, June 2025, American Chemical Society (ACS)

    Dr Alberto Perez

  6. PERRC: Protease Engineering with Reactant Residence Time Control

    Article • ACS Synthetic Biology, May 2025, American Chemical Society (ACS)

    Dr Alberto Perez

  7. The need to implement FAIR principles in biomolecular simulations

    Article • Nature Chemical Biology, April 2025, Springer Science + Business Media

    Dr Alberto Perez

  8. Structural differentiation of protein charge state conformers via gas-phase ion/ion cross-linking mass spectrometry

    Article • International Journal of Mass Spectrometry, March 2025, Elsevier

    Dr Alberto Perez

  9. MELD in Action: Harnessing Data to Accelerate Molecular Dynamics

    Article • Journal of Chemical Information and Modeling, February 2025, American Chemical Society (ACS)

    Dr Alberto Perez

  10. Hybrid AI/physics pipeline for miniprotein binder prioritization: application to the BRD3 ET domain

    Article • Chemical Communications, January 2025, Royal Society of Chemistry

    Dr Alberto Perez

  11. RNA-Puzzles Round V: blind predictions of 23 RNA structures

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

    Dr Alberto Perez

  12. MELD-Adapt: On-the-Fly Belief Updating in Integrative Molecular Dynamics

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

    Dr Alberto Perez

  13. AlphaFold2knowssome protein folding principles

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Dr Alberto Perez

  14. Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices

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

    Dr Alberto Perez

  15. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

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

    Dr Alberto Perez

  16. A Computational Pipeline for Accurate Prioritization of Protein‐Protein Binding Candidates in High‐Throughput Protein Libraries

    Article • Angewandte Chemie, May 2024, Wiley

    Dr Alberto Perez

  17. A Computational Pipeline for Accurate Prioritization of Protein‐Protein Binding Candidates in High‐Throughput Protein Libraries

    Article • Angewandte Chemie, May 2024, Wiley

    Dr Alberto Perez

  18. Structural Elucidation of Ubiquitin via Gas-Phase Ion/Ion Cross-Linking Reactions Using Sodium-Cationized Reagents Coupled with Infrared Multiphoton Dissociation

    Article • Analytical Chemistry, May 2024, American Chemical Society (ACS)

    Dr Alberto Perez

  19. Advancing Molecular Dynamics: Toward Standardization, Integration, and Data Accessibility in Structural Biology

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

    Dr Alberto Perez

  20. When MELD Meets GaMD: Accelerating Biomolecular Landscape Exploration

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

    Dr Alberto Perez

  21. GENERALIST: A latent space based generative model for protein sequence families

    Article • PLoS Computational Biology, November 2023, PLOS

    Dr Alberto Perez

  22. Revolutionizing peptide‐based drug discovery: Advances in the post‐AlphaFold era

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, November 2023, Wiley

    Dr Alberto Perez

  23. Hybrid computational methods combining experimental information with molecular dynamics

    Article • Current Opinion in Structural Biology, August 2023, Elsevier

    Dr Alberto Perez

  24. Biophysics at the dawn of exascale computers

    Article • Biophysical Journal, July 2023, Elsevier

    Dr Alberto Perez

  25. Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids

    Article • Cell Reports Medicine, May 2023, Elsevier

    Dr Alberto Perez

  26. CryoFold 2.0: Cryo-EM Structure Determination with MELD

    Article • The Journal of Physical Chemistry A, April 2023, American Chemical Society (ACS)

    Dr Alberto Perez

  27. Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work

    Article • Journal of Chemical Information and Modeling, April 2023, American Chemical Society (ACS)

    Dr Antonio Frontera, Dr Alberto Perez

  28. Structure Determination of Challenging Protein–Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations

    Article • Journal of Chemical Information and Modeling, March 2023, American Chemical Society (ACS)

    Dr Alberto Perez

  29. Molecular Modeling of Self-Assembling Peptides

    Article • ACS Applied Bio Materials, February 2023, American Chemical Society (ACS)

    Dr Alberto Perez

  30. Assessing a computational pipeline to identify binding motifs to the α2β1 integrin

    Article • Frontiers in Chemistry, February 2023, Frontiers

    Dr Alberto Perez

  31. Structural predictions of protein–DNA binding: MELD-DNA

    Article • Nucleic Acids Research, February 2023, Oxford University Press (OUP)

    Dr Alberto Perez

  32. Ranking Peptide Binders by Affinity with AlphaFold**

    Article • Angewandte Chemie, January 2023, Wiley

    Dr Alberto Perez

  33. Ranking Peptide Binders by Affinity with AlphaFold**

    Article • Angewandte Chemie, January 2023, Wiley

    Dr Alberto Perez

  34. Deciphering the Folding Mechanism of Proteins G and L and Their Mutants

    Article • Journal of the American Chemical Society, August 2022, American Chemical Society (ACS)

    Dr Alberto Perez

  35. A consensus view on the folding mechanism of protein G, L and their mutants

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Dr Alberto Perez

  36. AlphaFold encodes the principles to identify high affinity peptide binders

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Dr Alberto Perez

  37. Searching for Low Probability Opening Events in a DNA Sliding Clamp

    Article • Life, February 2022, MDPI AG

    Dr Alberto Perez

  38. Improving the analysis of biological ensembles through extended similarity measures

    Article • Physical Chemistry Chemical Physics, January 2022, Royal Society of Chemistry

    Dr Alberto Perez

  39. Modelling peptide–protein complexes: docking, simulations and machine learning

    Article • QRB Discovery, January 2022, Cambridge University Press

    Dr Alberto Perez

  40. Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets

    Article • Frontiers in Molecular Biosciences, November 2021, Frontiers

    Dr Alberto Perez

  41. Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

    Article • Biophysical Reviews, November 2021, Springer Science + Business Media

    Dr Alberto Perez

  42. Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment

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

    Dr Alberto Perez

  43. CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

    Article • Matter, October 2021, Elsevier

    Dr Alberto Perez

  44. Importance of Anion−π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study

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

    Dr Antonio Frontera, Dr Alberto Perez

  45. MELD-DNA: A new tool for capturing protein-DNA binding

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Dr Alberto Perez

  46. Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering

    Article • Frontiers in Molecular Biosciences, May 2021, Frontiers

    Dr Alberto Perez

  47. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

    Article • Nature Chemical Biology, February 2021, Springer Science + Business Media

    Dr Alberto Perez

  48. Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

    Article • Molecules, January 2021, MDPI AG

    Dr Alberto Perez

  49. Computing Ligands Bound to Proteins Using MELD-Accelerated MD

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

    Dr Alberto Perez

  50. NMR‐assisted protein structure prediction with MELDxMD

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

    Dr Alberto Perez

  51. High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid-State NMR Restraints

    Article • Angewandte Chemie, April 2019, Wiley

    Dr Alberto Perez

  52. Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge

    Article • Journal of Computer-Aided Molecular Design, November 2018, Springer Science + Business Media

    Dr Alberto Perez, Andrey Alekseenko

  53. MELD × MD Folds Nonthreadables, Giving Native Structures and Populations

    Article • Journal of Chemical Theory and Computation, November 2018, American Chemical Society (ACS)

    Dr Alberto Perez

  54. Allosterism and signal transfer in DNA

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

    Dr Alberto Perez

  55. MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths

    Article • Journal of Chemical Theory and Computation, March 2018, American Chemical Society (ACS)

    Dr Alberto Perez

  56. Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding

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

    Dr Alberto Perez

  57. Regulation of the activity of the promoter of RNA-induced silencing, C3PO

    Article • Protein Science, July 2017, Wiley

    Suzanne Scarlata, Dr Alberto Perez

  58. Accelerating physical simulations of proteins by leveraging external knowledge

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, April 2017, Wiley

    Dr Alberto Perez

  59. Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics

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

    Dr Alberto Perez

  60. Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX

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

    Dr Alberto Perez

  61. Blind protein structure prediction using accelerated free-energy simulations

    Article • Science Advances, November 2016, American Association for the Advancement of Science

    Dr Alberto Perez

  62. Advances in free-energy-based simulations of protein folding and ligand binding

    Article • Current Opinion in Structural Biology, February 2016, Elsevier

    Dr Alberto Perez

  63. Constraint methods that accelerate free-energy simulations of biomolecules

    Article • The Journal of Chemical Physics, December 2015, American Institute of Physics

    Dr Alberto Perez

  64. Parmbsc1: a refined force field for DNA simulations

    Article • Nature Chemical Biology, November 2015, Nature

    Professor Josep Ll. Gelpi, Dr Alberto Perez, Professor Michele Vendruscolo

  65. Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations

    Article • Journal of Chemical Theory and Computation, October 2015, American Chemical Society (ACS)

    Dr Alberto Perez

  66. The lipid raft proteome ofBorrelia burgdorferi

    Article • PROTEOMICS, September 2015, Wiley

    Dr Alberto Perez

  67. Accelerating molecular simulations of proteins using Bayesian inference on weak information

    Article • Proceedings of the National Academy of Sciences, September 2015, Proceedings of the National Academy of Sciences

    Dr Alberto Perez

  68. Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins

    Article • Journal of Chemical Theory and Computation, August 2015, American Chemical Society (ACS)

    Dr Alberto Perez

  69. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference

    Article • Proceedings of the National Academy of Sciences, May 2015, Proceedings of the National Academy of Sciences

    Dr Alberto Perez

  70.  ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

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

    Dr Alberto Perez

  71. Extracting representative structures from protein conformational ensembles

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

    Dr Alberto Perez

  72. Computing the Relative Stabilities and the Per-Residue Components in Protein Conformational Changes

    Article • Structure, January 2014, Elsevier

    Dr Alberto Perez

  73. Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale

    Article • PLoS Computational Biology, December 2013, PLOS

    Professor Josep Ll. Gelpi, Dr Alberto Perez

  74. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

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

    Dr Alberto Perez

  75. FlexE: Using Elastic Network Models to Compare Models of Protein Structure

    Article • Journal of Chemical Theory and Computation, October 2012, American Chemical Society (ACS)

    Dr Alberto Perez

  76. Exploring polymorphisms in B-DNA helical conformations

    Article • Nucleic Acids Research, September 2012, Oxford University Press (OUP)

    Dr Alberto Perez

  77. Impact of Methylation on the Physical Properties of DNA

    Article • Biophysical Journal, May 2012, Elsevier

    Dr Alberto Perez, Ramon Eritja

  78. Frontiers in Molecular Dynamics Simulations of DNA

    Article • Accounts of Chemical Research, February 2012, American Chemical Society (ACS)

    Dr Alberto Perez

  79. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

    Article • BMC Genomics, January 2011, Springer Science + Business Media

    Dr Alberto Perez

  80. Assessment of protein structure refinement in CASP9

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

    Dr Alberto Perez

  81. MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

    Article • Structure, November 2010, Elsevier

    Professor Josep Ll. Gelpi, Dr Alberto Perez, Marco D'Abramo

  82. Toward a Consensus View of Duplex RNA Flexibility

    Article • Biophysical Journal, September 2010, Elsevier

    Dr Alberto Perez

  83. Real-Time Atomistic Description of DNA Unfolding

    Article • Angewandte Chemie, May 2010, Wiley

    Dr Alberto Perez

  84. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

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

    Dr Alberto Perez

  85. Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids

    Article • The Journal of Physical Chemistry, July 2008, American Chemical Society (ACS)

    Dr Alberto Perez

  86. DNAlive: a tool for the physical analysis of DNA at the genomic scale

    Article • Bioinformatics, June 2008, Oxford University Press (OUP)

    Dr Alberto Perez

  87. Recent advances in the study of nucleic acid flexibility by molecular dynamics

    Article • Current Opinion in Structural Biology, April 2008, Elsevier

    Dr Alberto Perez

  88. Towards a molecular dynamics consensus view of B-DNA flexibility

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

    Dr Alberto Perez

  89. 8-Amino guanine accelerates tetramolecular G-quadruplex formation

    Article • Chemical Communications, January 2008, Royal Society of Chemistry

    Dr Alberto Perez, Ramon Eritja

  90. Dynamics of B-DNA on the Microsecond Time Scale

    Article • Journal of the American Chemical Society, November 2007, American Chemical Society (ACS)

    Dr Alberto Perez

  91. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers

    Article • Biophysical Journal, June 2007, Elsevier

    Dr Alberto Perez

  92. Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water

    Article • Nucleic Acids Research, April 2007, Oxford University Press (OUP)

    Dr Alberto Perez

  93. A consensus view of protein dynamics

    Article • Proceedings of the National Academy of Sciences, January 2007, Proceedings of the National Academy of Sciences

    Professor Josep Ll. Gelpi, Dr Alberto Perez

  94. Determining promoter location based on DNA structure first-principles calculations

    Article • Genome Biology, January 2007, Springer Science + Business Media

    Dr Alberto Perez

  95. Essential Dynamics:  A Tool for Efficient Trajectory Compression and Management

    Article • Journal of Chemical Theory and Computation, March 2006, American Chemical Society (ACS)

    Dr Alberto Perez

  96. Data Mining of Molecular Dynamics Trajectories of Nucleic Acids

    Article • Journal of Biomolecular Structure and Dynamics, February 2006, Taylor & Francis

    Dr Alberto Perez

  97. Data Mining of Molecular Dynamic Trajectories of Nucleic Acids

    Article • January 2006, Springer Science + Business Media

    Dr Alberto Perez

  98. Exploring the Essential Dynamics of B-DNA

    Article • Journal of Chemical Theory and Computation, September 2005, American Chemical Society (ACS)

    Dr Alberto Perez

  99. Are the Hydrogen Bonds of RNA (A⋅U) Stronger Than those of DNA (A⋅T)? A Quantum Mechanics Study

    Article • Chemistry - A European Journal, August 2005, Wiley

    Dr Alberto Perez

  100. Structure, Recognition Properties, and Flexibility of the DNA·RNA Hybrid

    Article • Journal of the American Chemical Society, April 2005, American Chemical Society (ACS)

    Dr Alberto Perez

  101. Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

    Article • Journal of Molecular Biology, October 2004, Elsevier

    Dr Alberto Perez

  102. The relative flexibility of B-DNA and A-RNA duplexes: database analysis

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

    Dr Alberto Perez

  103. Theoretical methods for the simulation of nucleic acids

    Article • Chemical Society Reviews, January 2003, Royal Society of Chemistry

    Dr Alberto Perez