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.
175 related articles for article (PubMed ID: 30289712)
1. Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages. Loeffler HH; Bosisio S; Duarte Ramos Matos G; Suh D; Roux B; Mobley DL; Michel J J Chem Theory Comput; 2018 Nov; 14(11):5567-5582. PubMed ID: 30289712 [TBL] [Abstract][Full Text] [Related]
2. Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations. Nelson L; Bariami S; Ringrose C; Horton JT; Kurdekar V; Mey ASJS; Michel J; Cole DJ J Chem Inf Model; 2021 May; 61(5):2124-2130. PubMed ID: 33886305 [TBL] [Abstract][Full Text] [Related]
3. A Python tool to set up relative free energy calculations in GROMACS. Klimovich PV; Mobley DL J Comput Aided Mol Des; 2015 Nov; 29(11):1007-14. PubMed ID: 26487189 [TBL] [Abstract][Full Text] [Related]
4. 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]
5. Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program. Wieder M; Fleck M; Braunsfeld B; Boresch S J Comput Chem; 2022 Jun; 43(17):1151-1160. PubMed ID: 35485139 [TBL] [Abstract][Full Text] [Related]
6. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. Matos GDR; Kyu DY; Loeffler HH; Chodera JD; Shirts MR; Mobley DL J Chem Eng Data; 2017 May; 62(5):1559-1569. PubMed ID: 29056756 [TBL] [Abstract][Full Text] [Related]
7. EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules. Cao S; Kalin ML; Huang X J Comput Chem; 2023 Jun; 44(17):1536-1549. PubMed ID: 36856731 [TBL] [Abstract][Full Text] [Related]
8. Polarizable Simulations with Second order Interaction Model - force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations. Kaminski GA; Ponomarev SY; Liu AB J Chem Theory Comput; 2009 Oct; 5(11):2935-2943. PubMed ID: 20209038 [TBL] [Abstract][Full Text] [Related]
9. Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field. Karwounopoulos J; Kaupang Å; Wieder M; Boresch S J Chem Theory Comput; 2023 Sep; 19(17):5988-5998. PubMed ID: 37616333 [TBL] [Abstract][Full Text] [Related]
10. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. Harger M; Li D; Wang Z; Dalby K; Lagardère L; Piquemal JP; Ponder J; Ren P J Comput Chem; 2017 Sep; 38(23):2047-2055. PubMed ID: 28600826 [TBL] [Abstract][Full Text] [Related]
11. Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007). Hafner J J Phys Condens Matter; 2008 Feb; 20(6):060301. PubMed ID: 21693862 [TBL] [Abstract][Full Text] [Related]
12. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. Shivakumar D; Deng Y; Roux B J Chem Theory Comput; 2009 Apr; 5(4):919-30. PubMed ID: 26609601 [TBL] [Abstract][Full Text] [Related]
13. 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]
14. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field. Shivakumar D; Williams J; Wu Y; Damm W; Shelley J; Sherman W J Chem Theory Comput; 2010 May; 6(5):1509-19. PubMed ID: 26615687 [TBL] [Abstract][Full Text] [Related]
15. Advancing Drug Discovery through Enhanced Free Energy Calculations. Abel R; Wang L; Harder ED; Berne BJ; Friesner RA Acc Chem Res; 2017 Jul; 50(7):1625-1632. PubMed ID: 28677954 [TBL] [Abstract][Full Text] [Related]
16. Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. Lee TS; Allen BK; Giese TJ; Guo Z; Li P; Lin C; McGee TD; Pearlman DA; Radak BK; Tao Y; Tsai HC; Xu H; Sherman W; York DM J Chem Inf Model; 2020 Nov; 60(11):5595-5623. PubMed ID: 32936637 [TBL] [Abstract][Full Text] [Related]
17. 1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies. Garrido NM; Queimada AJ; Jorge M; Macedo EA; Economou IG J Chem Theory Comput; 2009 Sep; 5(9):2436-46. PubMed ID: 26616624 [TBL] [Abstract][Full Text] [Related]
18. Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations. Lundborg M; Lindahl E J Phys Chem B; 2015 Jan; 119(3):810-23. PubMed ID: 25343332 [TBL] [Abstract][Full Text] [Related]