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Lingle Wang, Ph.D. - Publications

Affiliations: 
2012 Chemistry Columbia University, New York, NY 
Area:
Theory of liquids, molecular dynamics and Monte Carlo simulations of condensed matter
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51 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
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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