Alberto Perez
Alberto Perez
University of Florida, Department of Chemistry
Verified email at - Homepage
Cited by
Cited by
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 III, CA Laughton, ...
Biophysical journal 92 (11), 3817-3829, 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
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
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
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
Frontiers in molecular dynamics simulations of DNA
A Pérez, FJ Luque, M Orozco
Accounts of chemical research 45 (2), 196-205, 2012
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
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
Theoretical methods for the simulation of nucleic acids
M Orozco, A Pérez, A Noy, FJ Luque
Chemical Society Reviews 32 (6), 350-364, 2003
Determining promoter location based on DNA structure first-principles calculations
JR Gońi, A Pérez, D Torrents, M Orozco
Genome biology 8 (12), 1-10, 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
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
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
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
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories
T Meyer, M D'Abramo, A Hospital, M Rueda, C Ferrer-Costa, A Pérez, ...
Structure 18 (11), 1399-1409, 2010
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
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
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
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
Exploring polymorphisms in B-DNA helical conformations
PD Dans, A Perez, I Faustino, R Lavery, M Orozco
Nucleic acids research 40 (21), 10668-10678, 2012
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