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Julian Tirado-Rives
Julian Tirado-Rives
Senior Research Scientist, Yale University Department of Chemistry
Verified email at yale.edu - Homepage
Title
Cited by
Cited by
Year
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
WL Jorgensen, DS Maxwell, J Tirado-Rives
J Am Chem Soc 118 (45), 11225-11236, 1996
156591996
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
WL Jorgensen, J Tirado-Rives
Journal of the American Chemical Society 110 (6), 1657-1666, 1988
60291988
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
GA Kaminski, RA Friesner, J Tirado-Rives, WL Jorgensen
The Journal of Physical Chemistry B 105 (28), 6474-6487, 2001
43512001
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems
WL Jorgensen, J Tirado-Rives
Proceedings of the National Academy of Sciences 102 (19), 6665-6670, 2005
13972005
Performance of B3LYP density functional methods for a large set of organic molecules
J Tirado-Rives, WL Jorgensen
Journal of chemical theory and computation 4 (2), 297-306, 2008
13042008
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
LS Dodda, I Cabeza de Vaca, J Tirado-Rives, WL Jorgensen
Nucleic acids research 45 (W1), W331-W336, 2017
11072017
OPLS all‐atom force field for carbohydrates
W Damm, A Frontera, J Tirado–Rives, WL Jorgensen
Journal of computational chemistry 18 (16), 1955-1970, 1997
8841997
Improved peptide and protein torsional energetics with the OPLS-AA force field
MJ Robertson, J Tirado-Rives, WL Jorgensen
Journal of chemical theory and computation 11 (7), 3499-3509, 2015
7612015
1.14* CM1A-LBCC: localized bond-charge corrected CM1A charges for condensed-phase simulations
LS Dodda, JZ Vilseck, J Tirado-Rives, WL Jorgensen
The Journal of Physical Chemistry B 121 (15), 3864-3870, 2017
5542017
Molecular modeling of organic and biomolecular systems using BOSS and MCPRO
WL Jorgensen, J Tirado–Rives
Journal of Computational Chemistry 26 (16), 1689-1700, 2005
4882005
Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water
WL Jorgensen, JK Buckner, S Boudon, J Tirado‐Rives
The Journal of chemical physics 89 (6), 3742-3746, 1988
3711988
Methyl effects on protein–ligand binding
CS Leung, SSF Leung, J Tirado-Rives, WL Jorgensen
Journal of medicinal chemistry 55 (9), 4489-4500, 2012
3662012
Contribution of conformer focusing to the uncertainty in predicting free energies for protein− ligand binding
J Tirado-Rives, WL Jorgensen
Journal of medicinal chemistry 49 (20), 5880-5884, 2006
2942006
Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization
J Michel, J Tirado-Rives, WL Jorgensen
Journal of the American Chemical Society 131 (42), 15403-15411, 2009
2812009
Molecular dynamics simulations of the unfolding of an. alpha.-helical analog of ribonuclease A S-peptide in water
J Tirado-Rives, WL Jorgensen
Biochemistry 30 (16), 3864-3871, 1991
2661991
Monte Carlo vs molecular dynamics for conformational sampling
WL Jorgensen, J Tirado-Rives
The Journal of Physical Chemistry 100 (34), 14508-14513, 1996
2551996
Free energies of hydration from a generalized Born model and an ALL-atom force field
WL Jorgensen, JP Ulmschneider, J Tirado-Rives
The Journal of Physical Chemistry B 108 (41), 16264-16270, 2004
2422004
Prediction of the water content in protein binding sites
J Michel, J Tirado-Rives, WL Jorgensen
The journal of physical chemistry B 113 (40), 13337-13346, 2009
2362009
Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea
J Tirado-Rives, M Orozco, WL Jorgensen
Biochemistry 36 (24), 7313-7329, 1997
2231997
Potent noncovalent inhibitors of the main protease of SARS-CoV-2 from molecular sculpting of the drug perampanel guided by free energy perturbation calculations
CH Zhang, EA Stone, M Deshmukh, JA Ippolito, MM Ghahremanpour, ...
ACS central science 7 (3), 467-475, 2021
2202021
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