Year |
Citation |
Score |
2023 |
Hong RS, Rojas AV, Bhardwaj RM, Wang L, Mattei A, Abraham NS, Cusack KP, Pierce MO, Mondal S, Mehio N, Bordawekar S, Kym PR, Abel R, Sheikh AY. Free Energy Perturbation Approach for Accurate Crystalline Aqueous Solubility Predictions. Journal of Medicinal Chemistry. 66: 15883-15893. PMID 38016916 DOI: 10.1021/acs.jmedchem.3c01339 |
0.359 |
|
2023 |
Vögele M, Zhang BW, Kaindl J, Wang L. Is the Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding? Journal of Chemical Theory and Computation. PMID 37943175 DOI: 10.1021/acs.jctc.3c00899 |
0.494 |
|
2023 |
Ross GA, Lu C, Scarabelli G, Albanese SK, Houang E, Abel R, Harder ED, Wang L. The maximal and current accuracy of rigorous protein-ligand binding free energy calculations. Communications Chemistry. 6: 222. PMID 37838760 DOI: 10.1038/s42004-023-01019-9 |
0.779 |
|
2023 |
Salomon K, Abramyan AM, Plenge P, Wang L, Bundgaard C, Bang-Andersen B, Loland CJ, Shi L. Dynamic extracellular vestibule of human SERT: Unveiling druggable potential with high-affinity allosteric inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 120: e2304089120. PMID 37792512 DOI: 10.1073/pnas.2304089120 |
0.345 |
|
2023 |
Fajer M, Borrelli K, Abel R, Wang L. Quantitatively Accounting for Protein Reorganization in Computer-Aided Drug Design. Journal of Chemical Theory and Computation. PMID 37219932 DOI: 10.1021/acs.jctc.3c00009 |
0.453 |
|
2023 |
Chen W, Cui D, Jerome SV, Michino M, Lenselink EB, Huggins DJ, Beautrait A, Vendome J, Abel R, Friesner RA, Wang L. Enhancing Hit Discovery in Virtual Screening through Absolute Protein-Ligand Binding Free-Energy Calculations. Journal of Chemical Information and Modeling. PMID 37167486 DOI: 10.1021/acs.jcim.3c00013 |
0.519 |
|
2022 |
Coskun D, Chen W, Clark AJ, Lu C, Harder ED, Wang L, Friesner RA, Miller EB. Reliable and Accurate Prediction of Single-Residue p Values through Free Energy Perturbation Calculations. Journal of Chemical Theory and Computation. PMID 36384001 DOI: 10.1021/acs.jctc.2c00954 |
0.698 |
|
2022 |
Tresadern G, Tatikola K, Cabrera J, Wang L, Abel R, van Vlijmen H, Geys H. The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions. Journal of Chemical Information and Modeling. PMID 35061383 DOI: 10.1021/acs.jcim.1c01214 |
0.474 |
|
2021 |
Lu C, Wu C, Ghoreishi D, Chen W, Wang L, Damm W, Ross GA, Dahlgren MK, Russell E, Von Bargen CD, Abel R, Friesner RA, Harder ED. OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space. Journal of Chemical Theory and Computation. PMID 34096718 DOI: 10.1021/acs.jctc.1c00302 |
0.732 |
|
2021 |
Yu HS, Modugula K, Ichihara O, Kramschuster K, Keng S, Abel R, Wang L. General Theory of Fragment Linking in Molecular Design: Why Fragment Linking Rarely Succeeds and How to Improve Outcomes. Journal of Chemical Theory and Computation. 17: 450-462. PMID 33372778 DOI: 10.1021/acs.jctc.0c01004 |
0.445 |
|
2020 |
Albanese SK, Chodera JD, Volkamer A, Keng S, Abel R, Wang L. Is Structure-Based Drug Design Ready for Selectivity Optimization? Journal of Chemical Information and Modeling. PMID 33119284 DOI: 10.1021/acs.jcim.0c00815 |
0.352 |
|
2020 |
Ross GA, Russell E, Deng Y, Lu C, Harder ED, Abel R, Wang L. Enhancing water sampling in free energy calculations with grand canonical Monte Carlo. Journal of Chemical Theory and Computation. PMID 32955877 DOI: 10.1021/Acs.Jctc.0C00660 |
0.767 |
|
2020 |
Dajnowicz S, Ghoreishi D, Modugula K, Damm W, Harder ED, Abel R, Wang L, Yu HS. Advancing Free Energy Calculations of Metalloenzyme in Drug Discovery via Implementation of LFMM Potentials. Journal of Chemical Theory and Computation. PMID 32910652 DOI: 10.1021/Acs.Jctc.0C00615 |
0.773 |
|
2020 |
Paulsen JL, Yu HS, Sindhikara D, Wang L, Appleby TC, Villaseñor AG, Schmitz U, Shivakumar D. Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis. Journal of Chemical Information and Modeling. PMID 32539379 DOI: 10.1021/Acs.Jcim.0C00132 |
0.47 |
|
2020 |
Duan J, Lupyan D, Wang L. Improving the Accuracy of Protein Thermostability Predictions for Single Point Mutations. Biophysical Journal. PMID 32533939 DOI: 10.1016/J.Bpj.2020.05.020 |
0.437 |
|
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 |
0.395 |
|
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 |
0.739 |
|
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 |
0.641 |
|
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 |
0.502 |
|
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 |
0.756 |
|
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 |
0.585 |
|
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 |
0.563 |
|
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 |
0.422 |
|
2018 |
Wang L, Berne BJ. Efficient sampling of puckering states of monosaccharides through replica exchange with solute tempering and bond softening. The Journal of Chemical Physics. 149: 072306. PMID 30134707 DOI: 10.1063/1.5024389 |
0.559 |
|
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 |
0.396 |
|
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 |
0.614 |
|
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 |
0.794 |
|
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 |
0.608 |
|
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 |
0.461 |
|
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 |
0.768 |
|
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, ... ... Wang L, 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 |
0.622 |
|
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 |
0.494 |
|
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 |
0.629 |
|
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 |
0.468 |
|
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 |
0.571 |
|
2016 |
Mobley DL, Abel R, Wang L, Lim N. Examining how protein sampling impacts the convergence of relative binding free energy calculations F1000research. 5. DOI: 10.7490/F1000Research.1111982.1 |
0.506 |
|
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 |
0.773 |
|
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 |
0.792 |
|
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 |
0.784 |
|
2015 |
Gu Z, Yang Z, Wang L, Zhou H, Jimenez-Cruz CA, Zhou R. The role of basic residues in the adsorption of blood proteins onto the graphene surface. Scientific Reports. 5: 10873. PMID 26034971 DOI: 10.1038/Srep10873 |
0.5 |
|
2015 |
Liu S, Wang L, Mobley DL. Is ring breaking feasible in relative binding free energy calculations? Journal of Chemical Information and Modeling. 55: 727-35. PMID 25835054 DOI: 10.1021/Acs.Jcim.5B00057 |
0.512 |
|
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, 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 |
0.793 |
|
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 |
0.521 |
|
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 |
0.588 |
|
2012 |
Wang L, Berne BJ, Friesner RA. On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities. Proceedings of the National Academy of Sciences of the United States of America. 109: 1937-42. PMID 22308365 DOI: 10.1073/Pnas.1114017109 |
0.704 |
|
2011 |
Wang L, Friesner RA, Berne BJ. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). The Journal of Physical Chemistry. B. 115: 9431-8. PMID 21714551 DOI: 10.1021/Jp204407D |
0.524 |
|
2011 |
Wang L, Berne BJ, Friesner RA. Ligand binding to protein-binding pockets with wet and dry regions. Proceedings of the National Academy of Sciences of the United States of America. 108: 1326-30. PMID 21205906 DOI: 10.1073/Pnas.1016793108 |
0.668 |
|
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 |
0.672 |
|
2010 |
Wang L, Friesner RA, Berne BJ. Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models. Faraday Discussions. 146: 247-62; discussion 2. PMID 21043426 DOI: 10.1039/B925521B |
0.606 |
|
2010 |
Wang L, Friesner RA, Berne BJ. Competition of electrostatic and hydrophobic interactions between small hydrophobes and model enclosures. The Journal of Physical Chemistry. B. 114: 7294-301. PMID 20443643 DOI: 10.1021/Jp100772W |
0.579 |
|
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 |
0.507 |
|
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