Robert Abel
Robert Abel
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Comparison of multiple Amber force fields and development of improved protein backbone parameters
V Hornak, R Abel, A Okur, B Strockbine, A Roitberg, C Simmerling
Proteins: Structure, Function, and Bioinformatics 65 (3), 712-725, 2006
OPLS3: a force field providing broad coverage of drug-like small molecules and proteins
E Harder, W Damm, J Maple, C Wu, M Reboul, JY Xiang, L Wang, ...
Journal of chemical theory and computation 12 (1), 281-296, 2016
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field
L Wang, Y Wu, Y Deng, B Kim, L Pierce, G Krilov, D Lupyan, S Robinson, ...
Journal of the American Chemical Society 137 (7), 2695-2703, 2015
Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding
T Young, R Abel, B Kim, BJ Berne, RA Friesner
Proceedings of the National Academy of Sciences 104 (3), 808-813, 2007
Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
R Abel, T Young, R Farid, BJ Berne, RA Friesner
Journal of the American Chemical Society 130 (9), 2817-2831, 2008
The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling
J Li, R Abel, K Zhu, Y Cao, S Zhao, RA Friesner
Proteins: Structure, Function, and Bioinformatics 79 (10), 2794-2812, 2011
OPLS3e: Extending force field coverage for drug-like small molecules
K Roos, C Wu, W Damm, M Reboul, JM Stevenson, C Lu, MK Dahlgren, ...
Journal of chemical theory and computation 15 (3), 1863-1874, 2019
Docking covalent inhibitors: a parameter free approach to pose prediction and scoring
K Zhu, KW Borrelli, JR Greenwood, T Day, R Abel, RS Farid, E Harder
Journal of chemical information and modeling 54 (7), 1932-1940, 2014
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
T Beuming, Y Che, R Abel, B Kim, V Shanmugasundaram, W Sherman
Proteins: Structure, Function, and Bioinformatics 80 (3), 871-883, 2012
Modeling local structural rearrangements using FEP/REST: application to relative binding affinity predictions of CDK2 inhibitors
L Wang, Y Deng, JL Knight, Y Wu, B Kim, W Sherman, JC Shelley, T Lin, ...
Journal of chemical theory and computation 9 (2), 1282-1293, 2013
Prediction of protein–ligand binding poses via a combination of induced fit docking and metadynamics simulations
AJ Clark, P Tiwary, K Borrelli, S Feng, EB Miller, R Abel, RA Friesner, ...
Journal of chemical theory and computation 12 (6), 2990-2998, 2016
Contribution of explicit solvent effects to the binding affinity of small‐molecule inhibitors in blood coagulation factor serine proteases
R Abel, NK Salam, J Shelley, R Farid, RA Friesner, W Sherman
ChemMedChem 6 (6), 1049-1066, 2011
Advancing drug discovery through enhanced free energy calculations
R Abel, L Wang, ED Harder, BJ Berne, RA Friesner
Accounts of chemical research 50 (7), 1625-1632, 2017
Protein side-chain dynamics and residual conformational entropy
N Trbovic, JH Cho, R Abel, RA Friesner, M Rance, AG Palmer III
Journal of the American Chemical Society 131 (2), 615-622, 2009
Accurate binding free energy predictions in fragment optimization
TB Steinbrecher, M Dahlgren, D Cappel, T Lin, L Wang, G Krilov, R Abel, ...
Journal of chemical information and modeling 55 (11), 2411-2420, 2015
Prospective evaluation of free energy calculations for the prioritization of cathepsin L inhibitors
B Kuhn, M Tichý, L Wang, S Robinson, RE Martin, A Kuglstatter, J Benz, ...
Journal of medicinal chemistry 60 (6), 2485-2497, 2017
Predicting binding affinities for GPCR ligands using free-energy perturbation
EB Lenselink, J Louvel, AF Forti, JPD van Veldhoven, H de Vries, ...
ACS omega 1 (2), 293-304, 2016
Lead optimization mapper: automating free energy calculations for lead optimization
S Liu, Y Wu, T Lin, R Abel, JP Redmann, CM Summa, VR Jaber, NM Lim, ...
Journal of computer-aided molecular design 27 (9), 755-770, 2013
New hypotheses about the structure–function of proprotein convertase subtilisin/kexin type 9: Analysis of the epidermal growth factor‐like repeat A docking site using WaterMap
RA Pearlstein, QY Hu, J Zhou, D Yowe, J Levell, B Dale, VK Kaushik, ...
Proteins: Structure, Function, and Bioinformatics 78 (12), 2571-2586, 2010
Dewetting transitions in protein cavities
T Young, L Hua, X Huang, R Abel, R Friesner, BJ Berne
Proteins: Structure, Function, and Bioinformatics 78 (8), 1856-1869, 2010
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