All Stories

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

    Article • Angewandte Chemie International Edition, April 2019, Wiley

    Dr Alberto Perez

  2. 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

  3. 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

  4. 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

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

    Article • Protein Science, July 2017, Wiley

    Suzanne Scarlata, Dr Alberto Perez

  6. Accelerating physical simulations of proteins by leveraging external knowledge

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

    Dr Alberto Perez

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

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

    Dr Alberto Perez

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

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

    Dr Alberto Perez

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

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

    Dr Alberto Perez

  10. Parmbsc1: a refined force field for DNA simulations

    Article • Nature Methods, November 2015, Nature

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

  11. 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

  12. The lipid raft proteome ofBorrelia burgdorferi

    Article • PROTEOMICS, September 2015, Wiley

    Dr Alberto Perez

  13. 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

  14. 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

  15. 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

  16.  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

  17. Extracting representative structures from protein conformational ensembles

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

    Dr Alberto Perez

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

    Article • Structure, January 2014, Elsevier

    Dr Alberto Perez

  19. 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

  20. 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

  21. 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

  22. Exploring polymorphisms in B-DNA helical conformations

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

    Dr Alberto Perez

  23. Impact of Methylation on the Physical Properties of DNA

    Article • Biophysical Journal, May 2012, Elsevier

    Dr Alberto Perez, Ramon Eritja

  24. Frontiers in Molecular Dynamics Simulations of DNA

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

    Dr Alberto Perez

  25. 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

  26. Assessment of protein structure refinement in CASP9

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

    Dr Alberto Perez

  27. 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

  28. Toward a Consensus View of Duplex RNA Flexibility

    Article • Biophysical Journal, September 2010, Elsevier

    Dr Alberto Perez

  29. Real-Time Atomistic Description of DNA Unfolding

    Article • Angewandte Chemie International Edition, May 2010, Wiley

    Dr Alberto Perez

  30. 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

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

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

    Dr Alberto Perez

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

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

    Dr Alberto Perez

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

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

    Dr Alberto Perez

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

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

    Dr Alberto Perez

  35. 8-Amino guanine accelerates tetramolecular G-quadruplex formation

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

    Dr Alberto Perez, Ramon Eritja

  36. 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

  37. 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

  38. 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

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

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

    Dr Alberto Perez

  40. 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

  41. Data Mining of Molecular Dynamics Trajectories of Nucleic Acids

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

    Dr Alberto Perez

  42. Data Mining of Molecular Dynamic Trajectories of Nucleic Acids

    Article • January 2006, Springer Science + Business Media

    Dr Alberto Perez

  43. Exploring the Essential Dynamics of B-DNA

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

    Dr Alberto Perez

  44. 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

  45. 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

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

    Article • Journal of Molecular Biology, October 2004, Elsevier

    Dr Alberto Perez

  47. 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

  48. Theoretical methods for the simulation of nucleic acids

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

    Dr Alberto Perez