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.
279 related articles for article (PubMed ID: 28510433)
1. Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation. Ding X; Vilseck JZ; Hayes RL; Brooks CL J Chem Theory Comput; 2017 Jun; 13(6):2501-2510. PubMed ID: 28510433 [TBL] [Abstract][Full Text] [Related]
2. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis. Jiang W; Thirman J; Jo S; Roux B J Phys Chem B; 2018 Oct; 122(41):9435-9442. PubMed ID: 30253098 [TBL] [Abstract][Full Text] [Related]
3. Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations. Xie B; Nguyen TH; Minh DDL J Chem Theory Comput; 2017 Jun; 13(6):2930-2944. PubMed ID: 28430432 [TBL] [Abstract][Full Text] [Related]
4. Binding Free Energies of Host-Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation. Giovannelli E; Cioni M; Procacci P; Cardini G; Pagliai M; Volkov V; Chelli R J Chem Theory Comput; 2017 Dec; 13(12):5887-5899. PubMed ID: 29112430 [TBL] [Abstract][Full Text] [Related]
5. Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods. Hayes RL; Vilseck JZ; Brooks CL J Chem Theory Comput; 2022 Apr; 18(4):2114-2123. PubMed ID: 35255214 [TBL] [Abstract][Full Text] [Related]
6. Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics. Villarreal OD; Yu L; Rodriguez RA; Chen LY Biochem Biophys Res Commun; 2017 Jan; 483(1):203-208. PubMed ID: 28034750 [TBL] [Abstract][Full Text] [Related]
7. 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]
11. Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling. Robo MT; Hayes RL; Ding X; Pulawski B; Vilseck JZ Nat Commun; 2023 Dec; 14(1):8515. PubMed ID: 38129400 [TBL] [Abstract][Full Text] [Related]
12. Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD. Jiang W; Chipot C; Roux B J Chem Inf Model; 2019 Sep; 59(9):3794-3802. PubMed ID: 31411473 [TBL] [Abstract][Full Text] [Related]
13. A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. Hayes RL; Brooks CL J Comput Chem; 2021 Jun; 42(15):1088-1094. PubMed ID: 33844328 [TBL] [Abstract][Full Text] [Related]
14. An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. König G; Glaser N; Schroeder B; Kubincová A; Hünenberger PH; Riniker S J Chem Inf Model; 2020 Nov; 60(11):5407-5423. PubMed ID: 32794763 [TBL] [Abstract][Full Text] [Related]