299 related articles for article (PubMed ID: 33201701)
1. Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics.
Raman EP; Paul TJ; Hayes RL; Brooks CL
J Chem Theory Comput; 2020 Dec; 16(12):7895-7914. PubMed ID: 33201701
[TBL] [Abstract][Full Text] [Related]
2. Comprehensive, Open-Source, and Automated Workflow for Multisite λ-Dynamics in Lead Optimization.
Hu R; Zhang J; Kang Y; Wang Z; Pan P; Deng Y; Hsieh CY; Hou T
J Chem Theory Comput; 2024 Feb; 20(3):1465-1478. PubMed ID: 38300792
[TBL] [Abstract][Full Text] [Related]
3. Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations.
Armacost KA; Goh GB; Brooks CL
J Chem Theory Comput; 2015 Mar; 11(3):1267-77. PubMed ID: 26579773
[TBL] [Abstract][Full Text] [Related]
4. Protein-Ligand Binding Free Energy Calculations with FEP.
Wang L; Chambers J; Abel R
Methods Mol Biol; 2019; 2022():201-232. PubMed ID: 31396905
[TBL] [Abstract][Full Text] [Related]
5. Relative Binding Free Energy Calculations Applied to Protein Homology Models.
Cappel D; Hall ML; Lenselink EB; Beuming T; Qi J; Bradner J; Sherman W
J Chem Inf Model; 2016 Dec; 56(12):2388-2400. PubMed ID: 28024402
[TBL] [Abstract][Full Text] [Related]
6. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
Jo S; Jiang W; Lee HS; Roux B; Im W
J Chem Inf Model; 2013 Jan; 53(1):267-77. PubMed ID: 23205773
[TBL] [Abstract][Full Text] [Related]
7. Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches.
Raman EP; Lakkaraju SK; Denny RA; MacKerell AD
J Comput Chem; 2017 Jun; 38(15):1238-1251. PubMed ID: 27782307
[TBL] [Abstract][Full Text] [Related]
8. Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4.
Guest EE; Cervantes LF; Pickett SD; Brooks CL; Hirst JD
J Chem Inf Model; 2022 Mar; 62(6):1458-1470. PubMed ID: 35258972
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Accurate Binding Free Energy Predictions in Fragment Optimization.
Steinbrecher TB; Dahlgren M; Cappel D; Lin T; Wang L; Krilov G; Abel R; Friesner R; Sherman W
J Chem Inf Model; 2015 Nov; 55(11):2411-20. PubMed ID: 26457994
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.
Zhang H; Kim S; Giese TJ; Lee TS; Lee J; York DM; Im W
J Chem Inf Model; 2021 Sep; 61(9):4145-4151. PubMed ID: 34521199
[TBL] [Abstract][Full Text] [Related]
13. Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A
Stampelou M; Ladds G; Kolocouris A
J Phys Chem B; 2024 Feb; 128(4):914-936. PubMed ID: 38236582
[TBL] [Abstract][Full Text] [Related]
14. Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization.
Vilseck JZ; Cervantes LF; Hayes RL; Brooks CL
J Chem Inf Model; 2022 Mar; 62(6):1479-1488. PubMed ID: 35286093
[TBL] [Abstract][Full Text] [Related]
15. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
Deng N; Flynn WF; Xia J; Vijayan RS; Zhang B; He P; Mentes A; Gallicchio E; Levy RM
J Comput Aided Mol Des; 2016 Sep; 30(9):743-751. PubMed ID: 27562018
[TBL] [Abstract][Full Text] [Related]
16. E-novo: an automated workflow for efficient structure-based lead optimization.
Pearce BC; Langley DR; Kang J; Huang H; Kulkarni A
J Chem Inf Model; 2009 Jul; 49(7):1797-809. PubMed ID: 19552372
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1.
Vilseck JZ; Sohail N; Hayes RL; Brooks CL
J Phys Chem Lett; 2019 Sep; 10(17):4875-4880. PubMed ID: 31386370
[TBL] [Abstract][Full Text] [Related]
19. Advances in binding free energies calculations: QM/MM-based free energy perturbation method for drug design.
Rathore RS; Sumakanth M; Reddy MS; Reddanna P; Rao AA; Erion MD; Reddy MR
Curr Pharm Des; 2013; 19(26):4674-86. PubMed ID: 23260025
[TBL] [Abstract][Full Text] [Related]
20. Accurate calculation of absolute free energy of binding for SHP2 allosteric inhibitors using free energy perturbation.
Liang L; Liu H; Xing G; Deng C; Hua Y; Gu R; Lu T; Chen Y; Zhang Y
Phys Chem Chem Phys; 2022 May; 24(17):9904-9920. PubMed ID: 35416820
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]