Robert Abel, Ph.D. - Publications

Affiliations: 
2009 Columbia University, New York, NY 
Area:
Computational Chemistry

48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 de Oliveira C, Yu HS, Chen W, Abel R, Wang L. Correction to "Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States". Journal of Chemical Theory and Computation. PMID 31550159 DOI: 10.1021/acs.jctc.9b00841  0.52
2019 Yu HS, Gao C, Lupyan D, Wu Y, Kimura T, Wu C, Jacobson L, Harder ED, Abel R, Wang L. Towards Atomistic Modelling of Irreversible Covalent Inhibitor Binding Kinetics. Journal of Chemical Information and Modeling. PMID 31425654 DOI: 10.1021/acs.jcim.9b00268  0.52
2019 Wang L, Chambers J, Abel R. Protein-Ligand Binding Free Energy Calculations with FEP. Methods in Molecular Biology (Clifton, N.J.). 2022: 201-232. PMID 31396905 DOI: 10.1007/978-1-4939-9608-7_9  0.52
2019 Clark AJ, Negron C, Hauser K, Sun M, Wang L, Abel R, Friesner RA. Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces. Journal of Molecular Biology. PMID 30776430 DOI: 10.1016/j.jmb.2019.02.003  0.72
2019 Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, Dahlgren MK, Mondal S, Chen W, Wang L, Abel R, Friesner RA, Harder ED. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. Journal of Chemical Theory and Computation. PMID 30768902 DOI: 10.1021/acs.jctc.8b01026  0.72
2018 de Oliveira C, Yu HS, Chen W, Abel R, Wang L. A Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States. Journal of Chemical Theory and Computation. PMID 30537823 DOI: 10.1021/acs.jctc.8b00826  0.52
2018 Chen W, Deng Y, Russell E, Wu Y, Abel R, Wang L. Accurate calculation of relative binding free energies between ligands with different net charges. Journal of Chemical Theory and Computation. PMID 30375870 DOI: 10.1021/acs.jctc.8b00825  0.52
2018 Abel R, Manas ES, Friesner RA, Farid RS, Wang L. Modeling the value of predictive affinity scoring in preclinical drug discovery. Current Opinion in Structural Biology. 52: 103-110. PMID 30321805 DOI: 10.1016/j.sbi.2018.09.002  0.72
2018 Hauser K, Negron C, Albanese SK, Ray S, Steinbrecher T, Abel R, Chodera JD, Wang L. Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations. Communications Biology. 1. PMID 30159405 DOI: 10.1101/239012  0.52
2018 He P, Zhang BW, Arasteh S, Wang L, Abel R, Levy RM. Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. The Journal of Physical Chemistry Letters. PMID 30024165 DOI: 10.1021/acs.jpclett.8b01851  0.52
2017 Yu HS, Deng Y, Wu Y, Sindhikara D, Rask AR, Kimura T, Abel R, Wang L. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets. Journal of Chemical Theory and Computation. PMID 29120625 DOI: 10.1021/acs.jctc.7b00885  0.52
2017 Abel R, Wang L, Harder ED, Berne BJ, Friesner RA. Advancing Drug Discovery through Enhanced Free Energy Calculations. Accounts of Chemical Research. PMID 28677954 DOI: 10.1021/acs.accounts.7b00083  0.72
2017 Abel R, Wang L, Mobley DL, Friesner RA. A Critical Review of Validation, Blind Testing, and Real-World Use of Alchemical Protein-Ligand Binding Free Energy Calculations. Current Topics in Medicinal Chemistry. PMID 28413950 DOI: 10.2174/1568026617666170414142131  0.72
2017 Kuhn B, Tichý M, Wang L, Robinson S, Martin RE, Kuglstatter A, Benz J, Giroud M, Schirmeister T, Abel R, Diederich F, Hert J. Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors. Journal of Medicinal Chemistry. PMID 28287264 DOI: 10.1021/acs.jmedchem.6b01881  0.52
2016 Lenselink EB, Louvel J, Forti AF, van Veldhoven JPD, de Vries H, Mulder-Krieger T, McRobb FM, Negri A, Goose J, Abel R, van Vlijmen HWT, Wang L, Harder E, Sherman W, IJzerman AP, et al. Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation. Acs Omega. 1: 293-304. PMID 30023478 DOI: 10.1021/acsomega.6b00086  0.52
2016 Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, ... ... Abel R, et al. 11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015. Journal of Cheminformatics. 8: 18. PMID 29270804 DOI: 10.1186/s13321-016-0119-5  0.52
2016 Steinbrecher T, Zhu C, Wang L, Abel R, Negron C, Pearlman D, Feyfant E, Duan J, Sherman W. Predicting the Effect of Amino Acid Single Point Mutations on Protein Stability - Large Scale Validation of MD-based Relative Free Energy Calculations. Journal of Molecular Biology. PMID 27964946 DOI: 10.1016/j.jmb.2016.12.007  0.52
2016 Wang L, Deng Y, Wu Y, Kim B, LeBard DN, Wandschneider D, Beachy M, Friesner RA, Abel R. Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery. Journal of Chemical Theory and Computation. PMID 27933808 DOI: 10.1021/acs.jctc.6b00991  0.72
2016 Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ, Zhou T, Kwong PD, Shapiro L, Honig B, Friesner RA. Free Energy Perturbation Calculation of Relative Binding Free energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1. Journal of Molecular Biology. PMID 27908641 DOI: 10.1016/j.jmb.2016.11.021  0.72
2016 Abel R, Mondal S, Masse C, Greenwood J, Harriman G, Ashwell MA, Bhat S, Wester R, Frye L, Kapeller R, Friesner RA. Accelerating drug discovery through tight integration of expert molecular design and predictive scoring. Current Opinion in Structural Biology. 43: 38-44. PMID 27816785 DOI: 10.1016/j.sbi.2016.10.007  0.72
2016 Lim NM, Wang L, Abel R, Mobley DL. Sensitivity in binding free energies due to protein reorganization. Journal of Chemical Theory and Computation. PMID 27462935 DOI: 10.1021/acs.jctc.6b00532  0.52
2016 Clark AJ, Tiwary P, Borrelli K, Feng S, Miller EB, Abel R, Friesner RA, Berne BJ. Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations. Journal of Chemical Theory and Computation. PMID 27145262 DOI: 10.1021/acs.jctc.6b00201  0.72
2016 Murphy RB, Repasky MP, Greenwood JR, Tubert-Brohman I, Jerome S, Annabhimoju R, Boyles NA, Schmitz CD, Abel R, Farid R, Friesner RA. WScore: A flexible and accurate treatment of explicit water molecules in ligand-receptor docking. Journal of Medicinal Chemistry. PMID 27054459 DOI: 10.1021/acs.jmedchem.6b00131  0.72
2015 Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti D, Krilov G, Jorgensen WL, Abel R, et al. OPLS3: a force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation. PMID 26584231 DOI: 10.1021/acs.jctc.5b00864  0.72
2015 Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W. Accurate Binding Free Energy Predictions in Fragment Optimization. Journal of Chemical Information and Modeling. PMID 26457994 DOI: 10.1021/acs.jcim.5b00538  0.72
2015 Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. Journal of Chemical Theory and Computation. 11: 2670-9. PMID 26085821 DOI: 10.1021/acs.jctc.5b00214  0.52
2015 Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, ... ... Abel R, et al. 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. Journal of the American Chemical Society. 137: 2695-703. PMID 25625324 DOI: 10.1021/ja512751q  0.72
2015 Stafford KA, Trbovic N, Butterwick JA, Abel R, Friesner RA, Palmer AG. Conformational preferences underlying reduced activity of a thermophilic ribonuclease H. Journal of Molecular Biology. 427: 853-66. PMID 25550198 DOI: 10.1016/j.jmb.2014.11.023  0.72
2015 Goldfeld DA, Murphy R, Kim B, Wang L, Beuming T, Abel R, Friesner RA. Docking and free energy perturbation studies of ligand binding in the kappa opioid receptor. The Journal of Physical Chemistry. B. 119: 824-35. PMID 25395044 DOI: 10.1021/jp5053612  0.72
2014 Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods. Journal of Chemical Theory and Computation. 10: 3207-20. PMID 26588291 DOI: 10.1021/ct500189s  0.72
2014 Zhu K, Borrelli KW, Greenwood JR, Day T, Abel R, Farid RS, Harder E. Docking covalent inhibitors: a parameter free approach to pose prediction and scoring. Journal of Chemical Information and Modeling. 54: 1932-40. PMID 24916536 DOI: 10.1021/ci500118s  0.72
2014 Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging data fusion strategies in multireceptor lead optimization MM/GBSA end-point methods Journal of Chemical Theory and Computation. 10: 3207-3220. DOI: 10.1021/ct500189s  0.72
2013 Wang L, Deng Y, Knight JL, Wu Y, Kim B, Sherman W, Shelley JC, Lin T, Abel R. Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors. Journal of Chemical Theory and Computation. 9: 1282-93. PMID 26588769 DOI: 10.1021/ct300911a  0.72
2013 Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL. Lead optimization mapper: automating free energy calculations for lead optimization. Journal of Computer-Aided Molecular Design. 27: 755-70. PMID 24072356 DOI: 10.1007/s10822-013-9678-y  0.72
2013 Friesner RA, Abel R, Goldfeld DA, Miller EB, Murrett CS. Computational methods for high resolution prediction and refinement of protein structures. Current Opinion in Structural Biology. 23: 177-84. PMID 23688933 DOI: 10.1016/j.sbi.2013.01.010  0.72
2013 Pearlstein RA, Sherman W, Abel R. Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors. Proteins. 81: 1509-26. PMID 23468227 DOI: 10.1002/prot.24276  0.72
2012 Beuming T, Che Y, Abel R, Kim B, Shanmugasundaram V, Sherman W. Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization. Proteins. 80: 871-83. PMID 22223256 DOI: 10.1002/prot.23244  0.72
2012 Penfold TJ, Tavernelli I, Abel R, Rothlisberger U, Chergui M. Simulations of ground and excited state X-ray absorption spectra for molecules in solution: The role of the solvent International Conference On Ultrafast Structural Dynamics, Icusd 2012 0.72
2011 Li J, Abel R, Zhu K, Cao Y, Zhao S, Friesner RA. The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins. 79: 2794-812. PMID 21905107 DOI: 10.1002/prot.23106  0.72
2011 Abel R, Salam NK, Shelley J, Farid R, Friesner RA, Sherman W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases. Chemmedchem. 6: 1049-66. PMID 21506273 DOI: 10.1002/cmdc.201000533  0.72
2010 Abel R, Wang L, Friesner RA, Berne BJ. A displaced-solvent functional analysis of model hydrophobic enclosures. Journal of Chemical Theory and Computation. 6: 2924-2934. PMID 21135914 DOI: 10.1021/ct100215c  0.72
2010 Pearlstein RA, Hu QY, Zhou J, Yowe D, Levell J, Dale B, Kaushik VK, Daniels D, Hanrahan S, Sherman W, Abel R. 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. Proteins. 78: 2571-86. PMID 20589640 DOI: 10.1002/prot.22767  0.72
2010 Young T, Hua L, Huang X, Abel R, Friesner R, Berne BJ. Dewetting transitions in protein cavities. Proteins. 78: 1856-69. PMID 20225258 DOI: 10.1002/prot.22699  0.72
2009 Wang L, Abel R, Friesner RA, Berne BJ. Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid. Journal of Chemical Theory and Computation. 5: 1462-1473. PMID 19851475 DOI: 10.1021/ct900078k  0.72
2009 Trbovic N, Cho JH, Abel R, Friesner RA, Rance M, Palmer AG. Protein side-chain dynamics and residual conformational entropy. Journal of the American Chemical Society. 131: 615-22. PMID 19105660 DOI: 10.1021/ja806475k  0.72
2008 Abel R, Young T, Farid R, Berne BJ, Friesner RA. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. Journal of the American Chemical Society. 130: 2817-31. PMID 18266362 DOI: 10.1021/ja0771033  0.72
2007 Young T, Abel R, Kim B, Berne BJ, Friesner RA. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proceedings of the National Academy of Sciences of the United States of America. 104: 808-13. PMID 17204562 DOI: 10.1073/pnas.0610202104  0.72
2006 Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 65: 712-25. PMID 16981200 DOI: 10.1002/prot.21123  0.72
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