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.
24. 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]
25. Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics. Shinobu A; Re S; Sugita Y Front Mol Biosci; 2022; 9():878830. PubMed ID: 35573746 [TBL] [Abstract][Full Text] [Related]
26. Potential-based dynamical reweighting for Markov state models of protein dynamics. Weber JK; Pande VS J Chem Theory Comput; 2015 Jun; 11(6):2412-20. PubMed ID: 26575541 [TBL] [Abstract][Full Text] [Related]
27. Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages. Hu Y; Hong W; Shi Y; Liu H J Chem Theory Comput; 2012 Oct; 8(10):3777-92. PubMed ID: 26593019 [TBL] [Abstract][Full Text] [Related]
29. Building maps in collective variable space. Gimondi I; Tribello GA; Salvalaglio M J Chem Phys; 2018 Sep; 149(10):104104. PubMed ID: 30219018 [TBL] [Abstract][Full Text] [Related]
30. Exploration of high dimensional free energy landscapes by a combination of temperature-accelerated sliced sampling and parallel biasing. Gupta A; Verma S; Javed R; Sudhakar S; Srivastava S; Nair NN J Comput Chem; 2022 Jun; 43(17):1186-1200. PubMed ID: 35510789 [TBL] [Abstract][Full Text] [Related]
31. Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics. Awasthi S; Kapil V; Nair NN J Comput Chem; 2016 Jun; 37(16):1413-24. PubMed ID: 27059305 [TBL] [Abstract][Full Text] [Related]
32. Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling. Dokainish HM; Sugita Y Int J Mol Sci; 2020 Dec; 22(1):. PubMed ID: 33383937 [TBL] [Abstract][Full Text] [Related]
33. Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks. Hooft F; Pérez de Alba Ortíz A; Ensing B J Chem Theory Comput; 2021 Apr; 17(4):2294-2306. PubMed ID: 33662202 [TBL] [Abstract][Full Text] [Related]
34. Population based reweighting of scaled molecular dynamics. Sinko W; Miao Y; de Oliveira CA; McCammon JA J Phys Chem B; 2013 Oct; 117(42):12759-68. PubMed ID: 23721224 [TBL] [Abstract][Full Text] [Related]
35. Automated collective variable discovery for MFSD2A transporter from molecular dynamics simulations. Oh M; Rosa M; Xie H; Khelashvili G Biophys J; 2024 Sep; 123(17):2934-2955. PubMed ID: 38932456 [TBL] [Abstract][Full Text] [Related]
36. 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]
37. tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation. Oh M; da Hora GCA; Swanson JMJ J Chem Theory Comput; 2023 Dec; 19(23):8886-8900. PubMed ID: 37943658 [TBL] [Abstract][Full Text] [Related]
38. 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]
39. 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]
40. tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation. Oh M; da Hora GCA; Swanson JMJ bioRxiv; 2023 Aug; ():. PubMed ID: 37645884 [TBL] [Abstract][Full Text] [Related] [Previous] [Next] [New Search]