These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
162 related articles for article (PubMed ID: 37487138)
1. Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach. Baumann HM; Dybeck E; McClendon CL; Pickard FC; Gapsys V; Pérez-Benito L; Hahn DF; Tresadern G; Mathiowetz AM; Mobley DL J Chem Theory Comput; 2023 Aug; 19(15):5058-5076. PubMed ID: 37487138 [TBL] [Abstract][Full Text] [Related]
2. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. Cournia Z; Allen B; Sherman W J Chem Inf Model; 2017 Dec; 57(12):2911-2937. PubMed ID: 29243483 [TBL] [Abstract][Full Text] [Related]
3. Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study. Aldeghi M; Bodkin MJ; Knapp S; Biggin PC J Chem Inf Model; 2017 Sep; 57(9):2203-2221. PubMed ID: 28786670 [TBL] [Abstract][Full Text] [Related]
4. Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. Chen L; Wu Y; Wu C; Silveira A; Sherman W; Xu H; Gallicchio E J Chem Inf Model; 2024 Jan; 64(1):250-264. PubMed ID: 38147877 [TBL] [Abstract][Full Text] [Related]
5. Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations. Musleh S; Alibay I; Biggin PC; Bryce RA J Chem Inf Model; 2024 Oct; 64(20):8063-8073. PubMed ID: 39413277 [TBL] [Abstract][Full Text] [Related]
6. Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach. Tsai HC; Xu J; Guo Z; Yi Y; Tian C; Que X; Giese T; Lee TS; York DM; Ganguly A; Pan A J Chem Inf Model; 2024 Sep; 64(18):7046-7055. PubMed ID: 39225694 [TBL] [Abstract][Full Text] [Related]
7. Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols. Bhati AP; Coveney PV J Chem Theory Comput; 2022 Apr; 18(4):2687-2702. PubMed ID: 35293737 [TBL] [Abstract][Full Text] [Related]
8. Convergence-Adaptive Roundtrip Method Enables Rapid and Accurate FEP Calculations. Yao Y; Liu R; Li W; Huang W; Lai Y; Luo HB; Li Z J Chem Theory Comput; 2024 Sep; ():. PubMed ID: 39236257 [TBL] [Abstract][Full Text] [Related]
9. Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations. Cappel D; Jerome S; Hessler G; Matter H J Chem Inf Model; 2020 Mar; 60(3):1432-1444. PubMed ID: 31986249 [TBL] [Abstract][Full Text] [Related]
10. Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery. Wang L; Deng Y; Wu Y; Kim B; LeBard DN; Wandschneider D; Beachy M; Friesner RA; Abel R J Chem Theory Comput; 2017 Jan; 13(1):42-54. PubMed ID: 27933808 [TBL] [Abstract][Full Text] [Related]
12. Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations. Ries B; Alibay I; Swenson DWH; Baumann HM; Henry MM; Eastwood JRB; Gowers RJ J Chem Theory Comput; 2024 Mar; 20(5):1862-1877. PubMed ID: 38330251 [TBL] [Abstract][Full Text] [Related]
13. Free energy perturbation (FEP)-guided scaffold hopping. Wu D; Zheng X; Liu R; Li Z; Jiang Z; Zhou Q; Huang Y; Wu XN; Zhang C; Huang YY; Luo HB Acta Pharm Sin B; 2022 Mar; 12(3):1351-1362. PubMed ID: 35530128 [TBL] [Abstract][Full Text] [Related]
14. BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations. Heinzelmann G; Huggins DJ; Gilson MK J Chem Theory Comput; 2024 Aug; 20(15):6518-6530. PubMed ID: 39088306 [TBL] [Abstract][Full Text] [Related]
15. Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method. Azimi S; Khuttan S; Wu JZ; Pal RK; Gallicchio E J Chem Inf Model; 2022 Jan; 62(2):309-323. PubMed ID: 34990555 [TBL] [Abstract][Full Text] [Related]
16. Absolute binding free energy calculations improve enrichment of actives in virtual compound screening. Feng M; Heinzelmann G; Gilson MK Sci Rep; 2022 Aug; 12(1):13640. PubMed ID: 35948614 [TBL] [Abstract][Full Text] [Related]
17. Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies. Zou J; Li Z; Liu S; Peng C; Fang D; Wan X; Lin Z; Lee TS; Raleigh DP; Yang M; Simmerling C J Chem Theory Comput; 2021 Jun; 17(6):3710-3726. PubMed ID: 34029468 [No Abstract] [Full Text] [Related]
18. Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules. Wahl J; Smieško M J Chem Inf Model; 2019 Feb; 59(2):754-765. PubMed ID: 30640456 [TBL] [Abstract][Full Text] [Related]
19. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. Kaus JW; Harder E; Lin T; Abel R; McCammon JA; Wang L J Chem Theory Comput; 2015 Jun; 11(6):2670-9. PubMed ID: 26085821 [TBL] [Abstract][Full Text] [Related]
20. Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites. Cruz J; Wickstrom L; Yang D; Gallicchio E; Deng N J Chem Theory Comput; 2020 Apr; 16(4):2803-2813. PubMed ID: 32101691 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]