| Year |
Citation |
Score |
| 2023 |
Caparotta M, Perez A. When MELD Meets GaMD: Accelerating Biomolecular Landscape Exploration. Journal of Chemical Theory and Computation. PMID 38039424 DOI: 10.1021/acs.jctc.3c01019 |
0.313 |
|
| 2023 |
Mondal A, Lenz S, MacCallum JL, Perez A. Hybrid computational methods combining experimental information with molecular dynamics. Current Opinion in Structural Biology. 81: 102609. PMID 37224642 DOI: 10.1016/j.sbi.2023.102609 |
0.341 |
|
| 2023 |
Mondal A, Swapna GVT, Lopez MM, Klang L, Hao J, Ma L, Roth MJ, Montelione GT, Perez A. Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. PMID 36988562 DOI: 10.1021/acs.jcim.2c01595 |
0.311 |
|
| 2023 |
Esmaeeli R, Bauzá A, Perez A. Structural predictions of protein-DNA binding: MELD-DNA. Nucleic Acids Research. PMID 36727436 DOI: 10.1093/nar/gkad013 |
0.379 |
|
| 2021 |
Shekhar M, Terashi G, Gupta C, Sarkar D, Debussche G, Sisco NJ, Nguyen J, Mondal A, Vant J, Fromme P, Van Horn WD, Tajkhorshid E, Kihara D, Dill K, Perez A, et al. CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps. Matter. 4: 3195-3216. PMID 35874311 DOI: 10.1016/j.matt.2021.09.004 |
0.571 |
|
| 2021 |
da Rosa G, Grille L, Calzada V, Ahmad K, Arcon JP, Battistini F, Bayarri G, Bishop T, Carloni P, Cheatham Iii T, Collepardo-Guevara R, Czub J, Espinosa JR, Galindo-Murillo R, Harris SA, et al. Sequence-dependent structural properties of B-DNA: what have we learned in 40 years? Biophysical Reviews. 13: 995-1005. PMID 35059023 DOI: 10.1007/s12551-021-00893-8 |
0.514 |
|
| 2021 |
Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, ... ... Perez A, et al. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods. PMID 33542514 DOI: 10.1038/s41592-020-01051-w |
0.427 |
|
| 2020 |
Liu C, Brini E, Perez A, Dill KA. Computing ligands bound to proteins using MELD-accelerated MD. Journal of Chemical Theory and Computation. PMID 32910647 DOI: 10.1021/Acs.Jctc.0C00543 |
0.523 |
|
| 2020 |
Nassar R, Perez A, Robertson JC, Liu C, Brini E, Dill KA. Determining Protein Structures using Accelerated MD Simulations and Noisy Data Biophysical Journal. 118: 141a. DOI: 10.1016/J.Bpj.2019.11.895 |
0.55 |
|
| 2020 |
Liu C, Brini E, Perez A, Dill KA. Computing Poses of Ligands Bound to Proteins using MELD Accelerated Molecular Dynamics Biophysical Journal. 118: 323a. DOI: 10.1016/J.Bpj.2019.11.1814 |
0.509 |
|
| 2019 |
Robertson JC, Nassar R, Liu C, Brini E, Dill KA, Perez A. NMR-assisted protein structure prediction with MELDxMD. Proteins. PMID 31350773 DOI: 10.1002/Prot.25788 |
0.546 |
|
| 2019 |
Perez A, Gaalswyk K, Jaroniec CP, MacCallum JL. High accuracy protein structures from minimal sparse paramagnetic solid-state NMR restraints. Angewandte Chemie (International Ed. in English). PMID 30913341 DOI: 10.1002/Anie.201811895 |
0.313 |
|
| 2019 |
Perez A, Shekhar M, Terashi G, Kihara D, Dill KA, Tajkhorshid E, Singharoy A. MAINMAST-MELD-MDFF: Denovo Structure-Determination with Data-Guided Molecular Dynamics Biophysical Journal. 116: 287a-288a. DOI: 10.1016/J.Bpj.2018.11.1553 |
0.507 |
|
| 2018 |
Ignatov M, Liu C, Alekseenko A, Sun Z, Padhorny D, Kotelnikov S, Kazennov A, Grebenkin I, Kholodov Y, Kolosvari I, Perez A, Dill K, Kozakov D. Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. Journal of Computer-Aided Molecular Design. PMID 30421350 DOI: 10.1007/S10822-018-0176-0 |
0.468 |
|
| 2018 |
Robertson JC, Perez A, Dill KA. MELD x MD Folds Nonthreadables, Giving Native Structures and Populations. Journal of Chemical Theory and Computation. PMID 30407805 DOI: 10.1021/Acs.Jctc.8B00886 |
0.55 |
|
| 2018 |
Balaceanu A, Pérez A, Dans PD, Orozco M. Allosterism and signal transfer in DNA. Nucleic Acids Research. PMID 29905860 DOI: 10.1093/nar/gky549 |
0.493 |
|
| 2018 |
Perez A, Sittel F, Stock G, Dill KA. MELD-path efficiently computes conformational transitions, including multiple and diverse paths. Journal of Chemical Theory and Computation. PMID 29547695 DOI: 10.1021/Acs.Jctc.7B01294 |
0.482 |
|
| 2018 |
Robertson J, Perez A, Dill K. Meld Folds Nonthreadable Proteins Biophysical Journal. 114: 574a. DOI: 10.1016/J.Bpj.2017.11.3139 |
0.474 |
|
| 2017 |
Li J, Sagendorf JM, Chiu TP, Pasi M, Perez A, Rohs R. Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. Nucleic Acids Research. PMID 29165643 DOI: 10.1093/nar/gkx1145 |
0.309 |
|
| 2017 |
Perez A, Morrone JA, Dill KA. Accelerating physical simulations of proteins by leveraging external knowledge. Wiley Interdisciplinary Reviews. Computational Molecular Science. 7. PMID 28959358 DOI: 10.1002/Wcms.1309 |
0.58 |
|
| 2017 |
Morrone JA, Perez A, MacCallum JL, Dill KA. Computed binding of peptides to proteins with MELD-accelerated molecular dynamics. Journal of Chemical Theory and Computation. PMID 28042966 DOI: 10.1021/Acs.Jctc.6B00977 |
0.468 |
|
| 2017 |
Morrone JA, Perez A, Deng Q, Ha SN, Holloway MK, Sawyer TK, Sherborne BS, Brown FK, Dill KA. Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX. Journal of Chemical Theory and Computation. PMID 28042965 DOI: 10.1021/Acs.Jctc.6B00978 |
0.494 |
|
| 2016 |
Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA. Blind protein structure prediction using accelerated free-energy simulations. Science Advances. 2: e1601274. PMID 27847872 DOI: 10.1126/Sciadv.1601274 |
0.559 |
|
| 2016 |
Perez A, Morrone JA, Simmerling C, Dill KA. Advances in free-energy-based simulations of protein folding and ligand binding. Current Opinion in Structural Biology. 36: 25-31. PMID 26773233 DOI: 10.1016/J.Sbi.2015.12.002 |
0.558 |
|
| 2016 |
perez a, Brini E, Morrone J, Wagoner J, MacCallum J, Dill K. Combining Physics and Knowledge in Blind Protein Structure Prediction Biophysical Journal. 110: 345a. DOI: 10.1016/J.Bpj.2015.11.1855 |
0.547 |
|
| 2015 |
Perez A, MacCallum JL, Coutsias EA, Dill KA. Constraint methods that accelerate free-energy simulations of biomolecules. The Journal of Chemical Physics. 143: 243143. PMID 26723628 DOI: 10.1063/1.4936911 |
0.507 |
|
| 2015 |
Nguyen H, Pérez A, Bermeo S, Simmerling C. Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins. Journal of Chemical Theory and Computation. 11: 3714-28. PMID 26574454 DOI: 10.1021/Acs.Jctc.5B00271 |
0.325 |
|
| 2015 |
Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA. Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations. Journal of Chemical Theory and Computation. 11: 4770-9. PMID 26574266 DOI: 10.1021/Acs.Jctc.5B00662 |
0.505 |
|
| 2015 |
Ivani I, Dans PD, Noy A, Pérez A, Faustino I, Hospital A, Walther J, Andrio P, Goñi R, Balaceanu A, Portella G, Battistini F, Gelpí JL, González C, Vendruscolo M, et al. Parmbsc1: a refined force field for DNA simulations. Nature Methods. PMID 26569599 DOI: 10.1038/Nmeth.3658 |
0.506 |
|
| 2015 |
Perez A, MacCallum JL, Dill KA. Accelerating molecular simulations of proteins using Bayesian inference on weak information. Proceedings of the National Academy of Sciences of the United States of America. 112: 11846-51. PMID 26351667 DOI: 10.1073/Pnas.1515561112 |
0.601 |
|
| 2015 |
MacCallum JL, Perez A, Dill KA. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. Proceedings of the National Academy of Sciences of the United States of America. 112: 6985-90. PMID 26038552 DOI: 10.1073/Pnas.1506788112 |
0.524 |
|
| 2015 |
Nguyen H, Maier J, Huang H, Perrone V, Perez A, Simmerling C. Simulating Protein and Nucleic Acid Dynamics on the Microsecond to Millisecond Timescale Biophysical Journal. 108: 49a. DOI: 10.1016/J.Bpj.2014.11.302 |
0.388 |
|
| 2015 |
Perez A, MacCallum J, Dill KA. Using Physics and Heuristics in Protein Structure Prediction Biophysical Journal. 108: 210a. DOI: 10.1016/J.Bpj.2014.11.1164 |
0.565 |
|
| 2014 |
Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Pérez A, Petkevi?i?t? D, et al. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Research. 42: 12272-83. PMID 25260586 DOI: 10.1093/Nar/Gku855 |
0.503 |
|
| 2014 |
Perez A, Roy A, Kasavajhala K, Wagaman A, Dill KA, MacCallum JL. Extracting representative structures from protein conformational ensembles. Proteins. 82: 2671-80. PMID 24975328 DOI: 10.1002/Prot.24633 |
0.48 |
|
| 2014 |
Roy A, Perez A, Dill KA, Maccallum JL. Computing the relative stabilities and the per-residue components in protein conformational changes. Structure (London, England : 1993). 22: 168-75. PMID 24316402 DOI: 10.1016/J.Str.2013.10.015 |
0.547 |
|
| 2014 |
Perez A, MacCallum JL, Dill KA. Hydophobic Guided Protein Folding Biophysical Journal. 106: 438a. DOI: 10.1016/J.Bpj.2013.11.2466 |
0.529 |
|
| 2013 |
Dršata T, Pérez A, Orozco M, Morozov AV, Sponer J, Lankaš F. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of Chemical Theory and Computation. 9: 707-721. PMID 23976886 DOI: 10.1021/Ct300671Y |
0.569 |
|
| 2013 |
Perez A, MacCallum J, Dill K. 171 Protein structure prediction with limited data Journal of Biomolecular Structure and Dynamics. 31: 110-110. DOI: 10.1080/07391102.2013.786413 |
0.556 |
|
| 2013 |
Perez A, MacCallum J, Dill KA. Meld: Modeling Peptide-Protein Interactions Biophysical Journal. 104: 399a. DOI: 10.1016/J.Bpj.2012.11.2224 |
0.52 |
|
| 2012 |
Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL. FlexE: Using elastic network models to compare models of protein structure. Journal of Chemical Theory and Computation. 8: 3985-3991. PMID 25530735 DOI: 10.1021/Ct300148F |
0.519 |
|
| 2012 |
Dans PD, Pérez A, Faustino I, Lavery R, Orozco M. Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Research. 40: 10668-78. PMID 23012264 DOI: 10.1093/nar/gks884 |
0.529 |
|
| 2012 |
Pérez A, Luque FJ, Orozco M. Frontiers in molecular dynamics simulations of DNA. Accounts of Chemical Research. 45: 196-205. PMID 21830782 DOI: 10.1021/ar2001217 |
0.559 |
|
| 2012 |
MacCallum JL, Perez A, Dill KA. Physics Based Protein Structure Refinement Biophysical Journal. 102: 619a-620a. DOI: 10.1016/J.Bpj.2011.11.3376 |
0.557 |
|
| 2012 |
Perez A, MacCallum J, Hummel M, Coutsias E, Dill KA. Using Delaunay Tessellation of Proteins to Improve Current ENM Biophysical Journal. 102: 450a-451a. DOI: 10.1016/J.Bpj.2011.11.2471 |
0.531 |
|
| 2011 |
Deniz O, Flores O, Battistini F, Pérez A, Soler-López M, Orozco M. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. Bmc Genomics. 12: 489. PMID 21981773 DOI: 10.1186/1471-2164-12-489 |
0.449 |
|
| 2010 |
Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, Pérez A, Carrillo O, Camps J, Fenollosa C, Repchevsky D, Gelpí JL, Orozco M. MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. Structure (London, England : 1993). 18: 1399-409. PMID 21070939 DOI: 10.1016/j.str.2010.07.013 |
0.561 |
|
| 2010 |
Faustino I, Pérez A, Orozco M. Toward a consensus view of duplex RNA flexibility. Biophysical Journal. 99: 1876-85. PMID 20858433 DOI: 10.1016/j.bpj.2010.06.061 |
0.469 |
|
| 2010 |
Perez A, Orozco M. Real-time atomistic description of DNA unfolding. Angewandte Chemie (International Ed. in English). 49: 4805-8. PMID 20480472 DOI: 10.1002/anie.201000593 |
0.443 |
|
| 2010 |
Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, et al. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Research. 38: 299-313. PMID 19850719 DOI: 10.1093/Nar/Gkp834 |
0.547 |
|
| 2008 |
Gros J, Aviñó A, Lopez de la Osa J, González C, Lacroix L, Pérez A, Orozco M, Eritja R, Mergny JL. 8-Amino guanine accelerates tetramolecular G-quadruplex formation. Chemical Communications (Cambridge, England). 2926-8. PMID 18566727 DOI: 10.1039/B801221K |
0.384 |
|
| 2008 |
Svozil D, Sponer JE, Marchan I, Pérez A, Cheatham TE, Forti F, Luque FJ, Orozco M, Sponer J. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. The Journal of Physical Chemistry. B. 112: 8188-97. PMID 18558755 DOI: 10.1021/Jp801245H |
0.472 |
|
| 2008 |
Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M. DNAlive: a tool for the physical analysis of DNA at the genomic scale. Bioinformatics (Oxford, England). 24: 1731-2. PMID 18544548 DOI: 10.1093/bioinformatics/btn259 |
0.483 |
|
| 2008 |
Orozco M, Noy A, Pérez A. Recent advances in the study of nucleic acid flexibility by molecular dynamics. Current Opinion in Structural Biology. 18: 185-93. PMID 18304803 DOI: 10.1016/j.sbi.2008.01.005 |
0.45 |
|
| 2008 |
Pérez A, Lankas F, Luque FJ, Orozco M. Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Research. 36: 2379-94. PMID 18299282 DOI: 10.1093/nar/gkn082 |
0.54 |
|
| 2007 |
Goñi JR, Pérez A, Torrents D, Orozco M. Determining promoter location based on DNA structure first-principles calculations. Genome Biology. 8: R263. PMID 18072969 DOI: 10.1186/gb-2007-8-12-r263 |
0.505 |
|
| 2007 |
Pérez A, Luque FJ, Orozco M. Dynamics of B-DNA on the microsecond time scale. Journal of the American Chemical Society. 129: 14739-45. PMID 17985896 DOI: 10.1021/ja0753546 |
0.525 |
|
| 2007 |
Noy A, Pérez A, Laughton CA, Orozco M. Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water. Nucleic Acids Research. 35: 3330-8. PMID 17459891 DOI: 10.1093/nar/gkl1135 |
0.459 |
|
| 2007 |
Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophysical Journal. 92: 3817-29. PMID 17351000 DOI: 10.1529/Biophysj.106.097782 |
0.482 |
|
| 2007 |
Rueda M, Ferrer-Costa C, Meyer T, Pérez A, Camps J, Hospital A, Gelpí JL, Orozco M. A consensus view of protein dynamics. Proceedings of the National Academy of Sciences of the United States of America. 104: 796-801. PMID 17215349 DOI: 10.1073/pnas.0605534104 |
0.533 |
|
| 2006 |
Meyer T, Ferrer-Costa C, Pérez A, Rueda M, Bidon-Chanal A, Luque FJ, Laughton CA, Orozco M. Essential Dynamics: A Tool for Efficient Trajectory Compression and Management. Journal of Chemical Theory and Computation. 2: 251-8. PMID 26626512 DOI: 10.1021/ct050285b |
0.486 |
|
| 2006 |
Noy A, Meyer T, Rueda M, Ferrer C, Valencia A, Pérez A, de la Cruz X, López-Bes JM, Pouplana R, Fernandez-Recio J, Luque FJ, Orozco M. Data mining of molecular dynamics trajectories of nucleic acids. Journal of Biomolecular Structure & Dynamics. 23: 447-56. PMID 16363879 DOI: 10.1080/07391102.2006.10507070 |
0.489 |
|
| 2006 |
Pérez A, Sponer J, Jurecka P, Hobza P, Luque FJ, Orozco M. Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study. Chemistry (Weinheim An Der Bergstrasse, Germany). 11: 5062-6. PMID 15977281 DOI: 10.1002/Chem.200500255 |
0.424 |
|
| 2005 |
Pérez A, Blas JR, Rueda M, López-Bes JM, de la Cruz X, Orozco M. Exploring the Essential Dynamics of B-DNA. Journal of Chemical Theory and Computation. 1: 790-800. PMID 26641895 DOI: 10.1021/ct050051s |
0.521 |
|
| 2005 |
Noy A, Pérez A, Márquez M, Luque FJ, Orozco M. Structure, recognition properties, and flexibility of the DNA.RNA hybrid. Journal of the American Chemical Society. 127: 4910-20. PMID 15796556 DOI: 10.1021/ja043293v |
0.475 |
|
| 2004 |
Pérez A, Noy A, Lankas F, Luque FJ, Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Research. 32: 6144-51. PMID 15562006 DOI: 10.1093/nar/gkh954 |
0.484 |
|
| 2004 |
Noy A, Pérez A, Lankas F, Javier Luque F, Orozco M. Relative flexibility of DNA and RNA: a molecular dynamics study. Journal of Molecular Biology. 343: 627-38. PMID 15465050 DOI: 10.1016/j.jmb.2004.07.048 |
0.511 |
|
| 2003 |
Orozco M, Pérez A, Noy A, Luque FJ. Theoretical methods for the simulation of nucleic acids. Chemical Society Reviews. 32: 350-64. PMID 14671790 DOI: 10.1039/b207226m |
0.496 |
|
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