Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers A Pérez, I Marchán, D Svozil, J Sponer, TE Cheatham, CA Laughton, ... Biophysical journal 92 (11), 3817-3829, 2007 | 2396 | 2007 |
Parmbsc1: a refined force field for DNA simulations I Ivani, PD Dans, A Noy, A Pérez, I Faustino, A Hospital, J Walther, ... Nature methods 13 (1), 55-58, 2016 | 909 | 2016 |
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA R Lavery, K Zakrzewska, D Beveridge, TC Bishop, DA Case, ... Nucleic acids research 38 (1), 299-313, 2010 | 352 | 2010 |
Dynamics of B-DNA on the microsecond time scale A Pérez, FJ Luque, M Orozco Journal of the American Chemical Society 129 (47), 14739-14745, 2007 | 314 | 2007 |
Frontiers in molecular dynamics simulations of DNA A Pérez, FJ Luque, M Orozco Accounts of chemical research 45 (2), 196-205, 2012 | 259 | 2012 |
A consensus view of protein dynamics M Rueda, C Ferrer-Costa, T Meyer, A Pérez, J Camps, A Hospital, ... Proceedings of the National Academy of Sciences 104 (3), 796-801, 2007 | 237 | 2007 |
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA M Pasi, JH Maddocks, D Beveridge, TC Bishop, DA Case, T Cheatham III, ... Nucleic acids research 42 (19), 12272-12283, 2014 | 218 | 2014 |
Towards a molecular dynamics consensus view of B-DNA flexibility A Perez, F Lankas, FJ Luque, M Orozco Nucleic acids research 36 (7), 2379-2394, 2008 | 195 | 2008 |
Theoretical methods for the simulation of nucleic acids M Orozco, A Pérez, A Noy, FJ Luque Chemical Society Reviews 32 (6), 350-364, 2003 | 189 | 2003 |
Determining promoter location based on DNA structure first-principles calculations JR Goñi, A Pérez, D Torrents, M Orozco Genome biology 8 (12), R263, 2007 | 163 | 2007 |
Advances in free-energy-based simulations of protein folding and ligand binding A Perez, JA Morrone, C Simmerling, KA Dill Current opinion in structural biology 36, 25-31, 2016 | 161 | 2016 |
The relative flexibility of B-DNA and A-RNA duplexes: database analysis A Perez, A Noy, F Lankas, FJ Luque, M Orozco Nucleic acids research 32 (20), 6144-6151, 2004 | 154 | 2004 |
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference JL MacCallum, A Perez, KA Dill Proceedings of the National Academy of Sciences 112 (22), 6985-6990, 2015 | 151 | 2015 |
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories T Meyer, M D'Abramo, M Rueda, C Ferrer-Costa, A Pérez, O Carrillo, ... Structure 18 (11), 1399-1409, 2010 | 140 | 2010 |
Impact of methylation on the physical properties of DNA A Pérez, CL Castellazzi, F Battistini, K Collinet, O Flores, O Deniz, ... Biophysical journal 102 (9), 2140-2148, 2012 | 137 | 2012 |
Recent advances in the study of nucleic acid flexibility by molecular dynamics M Orozco, A Noy, A Pérez Current opinion in structural biology 18 (2), 185-193, 2008 | 134 | 2008 |
Essential dynamics: a tool for efficient trajectory compression and management T Meyer, C Ferrer-Costa, A Pérez, M Rueda, A Bidon-Chanal, FJ Luque, ... Journal of Chemical Theory and Computation 2 (2), 251-258, 2006 | 127 | 2006 |
Relative flexibility of DNA and RNA: a molecular dynamics study A Noy, A Perez, F Lankas, FJ Luque, M Orozco Journal of molecular biology 343 (3), 627-638, 2004 | 114 | 2004 |
Assessment of protein structure refinement in CASP9 JL MacCallum, A Pérez, MJ Schnieders, L Hua, MP Jacobson, KA Dill Proteins: Structure, Function, and Bioinformatics 79 (S10), 74-90, 2011 | 113 | 2011 |
Accelerating molecular simulations of proteins using Bayesian inference on weak information A Perez, JL MacCallum, KA Dill Proceedings of the National Academy of Sciences 112 (38), 11846-11851, 2015 | 111 | 2015 |