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.
6. Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity. Schulig L; Geist N; Delcea M; Link A; Kulke M J Chem Inf Model; 2022 Sep; 62(17):4200-4209. PubMed ID: 36004729 [TBL] [Abstract][Full Text] [Related]
7. Enhanced sampling and free energy calculations for protein simulations. Liao Q Prog Mol Biol Transl Sci; 2020; 170():177-213. PubMed ID: 32145945 [TBL] [Abstract][Full Text] [Related]
8. CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods. Suh D; Feng S; Lee H; Zhang H; Park SJ; Kim S; Lee J; Choi S; Im W Protein Sci; 2022 Nov; 31(11):e4446. PubMed ID: 36124940 [TBL] [Abstract][Full Text] [Related]
9. When MELD Meets GaMD: Accelerating Biomolecular Landscape Exploration. Caparotta M; Perez A J Chem Theory Comput; 2023 Dec; 19(23):8743-8750. PubMed ID: 38039424 [TBL] [Abstract][Full Text] [Related]
10. Collective Variables for Crystallization Simulations-from Early Developments to Recent Advances. Neha ; Tiwari V; Mondal S; Kumari N; Karmakar T ACS Omega; 2023 Jan; 8(1):127-146. PubMed ID: 36643553 [TBL] [Abstract][Full Text] [Related]
11. The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions. Pérez de Alba Ortíz A; Vreede J; Ensing B Methods Mol Biol; 2019; 2022():255-290. PubMed ID: 31396907 [TBL] [Abstract][Full Text] [Related]
12. Assessment and optimization of collective variables for protein conformational landscape: GB1 Ahalawat N; Mondal J J Chem Phys; 2018 Sep; 149(9):094101. PubMed ID: 30195312 [TBL] [Abstract][Full Text] [Related]
13. Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. Jung J; Kobayashi C; Sugita Y J Comput Chem; 2023 Jul; 44(20):1740-1749. PubMed ID: 37141320 [TBL] [Abstract][Full Text] [Related]
14. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review. Miao Y; McCammon JA Mol Simul; 2016; 42(13):1046-1055. PubMed ID: 27453631 [TBL] [Abstract][Full Text] [Related]
15. Replica exchange molecular dynamics method for protein folding simulation. Zhou R Methods Mol Biol; 2007; 350():205-23. PubMed ID: 16957325 [TBL] [Abstract][Full Text] [Related]
16. Increasing the Sampling Efficiency of Protein Conformational Change by Combining a Modified Replica Exchange Molecular Dynamics and Normal Mode Analysis. Peng C; Wang J; Shi Y; Xu Z; Zhu W J Chem Theory Comput; 2021 Jan; 17(1):13-28. PubMed ID: 33351613 [TBL] [Abstract][Full Text] [Related]
17. Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations. Kamiya M; Sugita Y J Chem Phys; 2018 Aug; 149(7):072304. PubMed ID: 30134668 [TBL] [Abstract][Full Text] [Related]
18. Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations. Rydzewski J; Chen M; Ghosh TK; Valsson O J Chem Theory Comput; 2022 Dec; 18(12):7179-7192. PubMed ID: 36367826 [TBL] [Abstract][Full Text] [Related]
19. Collective Variable-Based Enhanced Sampling: From Human Learning to Machine Learning. Fu H; Bian H; Shao X; Cai W J Phys Chem Lett; 2024 Feb; 15(6):1774-1783. PubMed ID: 38329095 [TBL] [Abstract][Full Text] [Related]
20. Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation. Shao Q; Shi J; Zhu W J Chem Theory Comput; 2017 Mar; 13(3):1229-1243. PubMed ID: 28121433 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]