| Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands L Chen, Y Wu, C Wu, A Silveira, W Sherman, H Xu, E Gallicchio Journal of Chemical Information and Modeling 64 (1), 250-264, 2023 | 10 | 2023 |
| Targeted protein degradation: advances, challenges, and prospects for computational methods B Mostofian, HJ Martin, A Razavi, S Patel, B Allen, W Sherman, ... Journal of Chemical Information and Modeling 63 (17), 5408-5432, 2023 | 13 | 2023 |
| Comprehensive Approach to Simulating Large Scale Conformational Changes in Biological Systems Utilizing a Path Collective Variable and New Barrier Restraint I Kolossváry, W Sherman The Journal of Physical Chemistry B 127 (23), 5214-5229, 2023 | 4 | 2023 |
| Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ... Nature communications 13 (1), 5884, 2022 | 37 | 2022 |
| A Different Kind of Restraint Suitable for Molecular Dynamics Simulations I Kolossváry, W Sherman biorxiv, 2022.08. 27.505552, 2022 | 1 | 2022 |
| Design of a systemic small molecule clinical STING agonist using physics-based simulations and artificial intelligence BK Allen, MM Kulkarni, B Chamberlain, T Dwight, C Koh, R Samant, ... Biorxiv, 2022.05. 23.493001, 2022 | 11 | 2022 |
| Precise binding free energy calculations for multiple molecules using an optimal measurement network of pairwise differences P Li, Z Li, Y Wang, H Dou, BK Radak, BK Allen, W Sherman, H Xu Journal of Chemical Theory and Computation 18 (2), 650-663, 2021 | 8 | 2021 |
| Fast equilibration of water between buried sites and the bulk by molecular dynamics with parallel Monte Carlo water moves on graphical processing units IY Ben-Shalom, C Lin, BK Radak, W Sherman, MK Gilson Journal of chemical theory and computation 17 (12), 7366-7372, 2021 | 19 | 2021 |
| Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones EB Nordquist, CA English, EM Clerico, W Sherman, LM Gierasch, J Chen PLOS Computational Biology 17 (11), e1009567, 2021 | 10 | 2021 |
| Atomic-resolution prediction of degrader-mediated ternary complex structures by combining molecular simulations with hydrogen deuterium exchange T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ... Biorxiv, 2021.09. 26.461830, 2021 | 12 | 2021 |
| System-level modeling of GPU/FPGA clusters for molecular dynamics simulations C Wu, S Bandara, T Geng, V Sachdeva, W Sherman, M Herbordt 2021 IEEE high performance extreme computing conference (HPEC), 1-8, 2021 | 11 | 2021 |
| Upgrade of fpga range-limited molecular dynamics to handle hundreds of processors C Wu, T Geng, S Bandara, C Yang, V Sachdeva, W Sherman, M Herbordt 2021 IEEE 29th Annual International Symposium on Field-Programmable Custom …, 2021 | 12 | 2021 |
| Free energy methods in drug discovery—introduction Z Cournia, C Chipot, B Roux, DM York, W Sherman Free energy methods in drug discovery: Current state and future directions, 1-38, 2021 | 36 | 2021 |
| Accounting for the central role of interfacial water in protein–ligand binding free energy calculations IY Ben-Shalom, Z Lin, BK Radak, C Lin, W Sherman, MK Gilson Journal of chemical theory and computation 16 (12), 7883-7894, 2020 | 29 | 2020 |
| A Communication-Efficient Multi-Chip Design for Range-Limited Molecular Dynamics C Wu, T Geng, C Yang, V Sachdeva, W Sherman, M Herbordt 2020 IEEE High Performance extreme Computing Conference (HPEC), 1-8, 2020 | 12 | 2020 |
| Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery TS Lee, BK Allen, TJ Giese, Z Guo, P Li, C Lin, TD McGee Jr, ... Journal of Chemical Information and Modeling 60 (11), 5595-5623, 2020 | 241 | 2020 |
| Oxoacridinyl acetic acid derivatives and methods of use BT Chamberlain, JM Rice, FE JERNIGAN III, W Sherman, MM Kulkarni, ... US Patent 10,745,358, 2020 | | 2020 |
| Improved alchemical free energy calculations with optimized smoothstep softcore potentials TS Lee, Z Lin, BK Allen, C Lin, BK Radak, Y Tao, HC Tsai, W Sherman, ... Journal of chemical theory and computation 16 (9), 5512-5525, 2020 | 52 | 2020 |
| Rigorous free energy simulations in virtual screening Z Cournia, BK Allen, T Beuming, DA Pearlman, BK Radak, W Sherman Journal of chemical information and modeling 60 (9), 4153-4169, 2020 | 150 | 2020 |
| Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger BJGE Pieters, MHM Wuts, J Poater, K Kumar, PB White, JJAG Kamps, ... Communications Chemistry 3 (1), 69, 2020 | 12 | 2020 |
Thijs BeumingLatham Biopharm Group在 lathambiopharm.com 的电子邮件经过验证
