Alberto Perez

Best Publications

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

  Alberto Pérez;Iván Marchán;Daniel Svozil;Daniel Svozil;Jiri Sponer;Jiri Sponer

  2508
  Citations

• Parmbsc1: a refined force field for DNA simulations

  Ivan Ivani;Pablo D Dans;Agnes Noy;Alberto Pérez

  1147
  Citations

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

  Richard Lavery;Krystyna Zakrzewska;David Beveridge;Thomas C. Bishop

  361
  Citations

• Dynamics of B-DNA on the microsecond time scale.

  Alberto Perez;F. Javier Luque;Modesto Orozco

  308
  Citations

• A consensus view of protein dynamics.

  Manuel Rueda;Carles Ferrer-Costa;Tim Meyer;Tim Meyer;Alberto Pérez

  292
  Citations

• Frontiers in Molecular Dynamics Simulations of DNA

  Alberto Pérez;F. Javier Luque;Modesto Orozco

  259
  Citations

• μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

  Marco Pasi;John H. Maddocks;David Beveridge;Thomas C. Bishop

  228
  Citations

• Theoretical methods for the simulation of nucleic acids.

  Modesto Orozco;Alberto Pérez;Agnes Noy;F. Javier Luque

  194
  Citations

• Towards a molecular dynamics consensus view of B-DNA flexibility

  Alberto Pérez;Filip Lankas;F. Javier Luque;Modesto Orozco

  191
  Citations

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

  Justin L. MacCallum;Alberto Perez;Ken A. Dill

  181
  Citations

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

  J Ramon Goñi;Alberto Pérez;David Torrents;Modesto Orozco

  170
  Citations

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

  Alberto Perez;Joseph A Morrone;Carlos Simmerling;Ken A Dill

  162
  Citations

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

  Tim Meyer;Marco D'Abramo;Manuel Rueda

  162
  Citations

• Impact of Methylation on the Physical Properties of DNA

  Alberto Pérez;Chiara Lara Castellazzi;Federica Battistini;Kathryn Collinet

  159
  Citations

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

  Alberto Pérez;Agnes Noy;Filip Lankas;F. Javier Luque

  158
  Citations

• Essential Dynamics: A Tool for Efficient Trajectory Compression and Management

  Meyer T;Ferrer-Costa C;Pérez A;Rueda M

  142
  Citations

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

  Modesto Orozco;Agnes Noy;Alberto Pérez

  132
  Citations

• Relative flexibility of DNA and RNA: a molecular dynamics study.

  Agnes Noy;Alberto Pérez;Filip Lankas;F. Javier Luque

  118
  Citations

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

  Jinsen Li;Jared M Sagendorf;Tsu-Pei Chiu;Marco Pasi

  116
  Citations

• Assessment of protein structure refinement in CASP9.

  Justin L. MacCallum;Alberto Pérez;Michael J. Schnieders;Lan Hua

  114
  Citations