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.
4. Enhanced molecular dynamics sampling of drug target conformations. Rodriguez-Bussey IG; Doshi U; Hamelberg D Biopolymers; 2016 Jan; 105(1):35-42. PubMed ID: 26352326 [TBL] [Abstract][Full Text] [Related]
5. Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations. Peng X; Zhang Y; Li Y; Liu Q; Chu H; Zhang D; Li G J Chem Theory Comput; 2018 Mar; 14(3):1216-1227. PubMed ID: 29394067 [TBL] [Abstract][Full Text] [Related]
6. Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations. Wereszczynski J; McCammon JA J Chem Theory Comput; 2010 Nov; 6(11):3285-3292. PubMed ID: 21072329 [TBL] [Abstract][Full Text] [Related]
7. Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. Fajer M; Hamelberg D; McCammon JA J Chem Theory Comput; 2008 Oct; 4(10):1565-1569. PubMed ID: 19461870 [TBL] [Abstract][Full Text] [Related]
8. 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]
9. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Hu H; Elstner M; Hermans J Proteins; 2003 Feb; 50(3):451-63. PubMed ID: 12557187 [TBL] [Abstract][Full Text] [Related]
10. Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding. Flores-Canales JC; Kurnikova M J Chem Theory Comput; 2015 Jun; 11(6):2550-9. PubMed ID: 26575554 [TBL] [Abstract][Full Text] [Related]
11. Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems. Nemec M; Hoffmann D J Chem Theory Comput; 2017 Feb; 13(2):400-414. PubMed ID: 28085284 [TBL] [Abstract][Full Text] [Related]
12. MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics. Yamamori Y; Kitao A J Chem Phys; 2013 Oct; 139(14):145105. PubMed ID: 24116651 [TBL] [Abstract][Full Text] [Related]
13. Gaussian Accelerated Molecular Dynamics in NAMD. Pang YT; Miao Y; Wang Y; McCammon JA J Chem Theory Comput; 2017 Jan; 13(1):9-19. PubMed ID: 28034310 [TBL] [Abstract][Full Text] [Related]
14. Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: accelerating with advanced extrapolation of effective solvation forces. Omelyan I; Kovalenko A J Chem Phys; 2013 Dec; 139(24):244106. PubMed ID: 24387356 [TBL] [Abstract][Full Text] [Related]
15. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface. Hu H; Lu Z; Parks JM; Burger SK; Yang W J Chem Phys; 2008 Jan; 128(3):034105. PubMed ID: 18205486 [TBL] [Abstract][Full Text] [Related]
16. Implementation of Accelerated Molecular Dynamics in NAMD. Wang Y; Harrison CB; Schulten K; McCammon JA Comput Sci Discov; 2011; 4(1):. PubMed ID: 21686063 [TBL] [Abstract][Full Text] [Related]
17. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. Miao Y; Sinko W; Pierce L; Bucher D; Walker RC; McCammon JA J Chem Theory Comput; 2014 Jul; 10(7):2677-2689. PubMed ID: 25061441 [TBL] [Abstract][Full Text] [Related]
18. Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the Φ, Ψ-conformational space of the α-(1-->2)-linked mannose disaccharide present in N- and O-linked glycoproteins. Säwén E; Massad T; Landersjö C; Damberg P; Widmalm G Org Biomol Chem; 2010 Aug; 8(16):3684-95. PubMed ID: 20574564 [TBL] [Abstract][Full Text] [Related]
19. Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study. de Oliveira CA; Hamelberg D; McCammon JA J Chem Phys; 2007 Nov; 127(17):175105. PubMed ID: 17994855 [TBL] [Abstract][Full Text] [Related]
20. A new force field (ECEPP-05) for peptides, proteins, and organic molecules. Arnautova YA; Jagielska A; Scheraga HA J Phys Chem B; 2006 Mar; 110(10):5025-44. PubMed ID: 16526746 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]