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. Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: application to enzyme adenylate kinase. Ramanathan A; Savol AJ; Agarwal PK; Chennubhotla CS Proteins; 2012 Nov; 80(11):2536-51. PubMed ID: 22733562 [TBL] [Abstract][Full Text] [Related]
5. Energy landscape of a native protein: jumping-among-minima model. Kitao A; Hayward S; Go N Proteins; 1998 Dec; 33(4):496-517. PubMed ID: 9849935 [TBL] [Abstract][Full Text] [Related]
6. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties. Li X; Hassan SA; Mehler EL Proteins; 2005 Aug; 60(3):464-84. PubMed ID: 15959866 [TBL] [Abstract][Full Text] [Related]
7. Characterizing global substates of myoglobin. Andrews BK; Romo T; Clarage JB; Pettitt BM; Phillips GN Structure; 1998 May; 6(5):587-94. PubMed ID: 9634696 [TBL] [Abstract][Full Text] [Related]
8. Conformational Sub-states and Populations in Enzyme Catalysis. Agarwal PK; Doucet N; Chennubhotla C; Ramanathan A; Narayanan C Methods Enzymol; 2016; 578():273-97. PubMed ID: 27497171 [TBL] [Abstract][Full Text] [Related]
9. Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains. Berg A; Franke L; Scheffner M; Peter C J Chem Theory Comput; 2020 May; 16(5):3205-3220. PubMed ID: 32196332 [TBL] [Abstract][Full Text] [Related]
10. Markov state models provide insights into dynamic modulation of protein function. Shukla D; Hernández CX; Weber JK; Pande VS Acc Chem Res; 2015 Feb; 48(2):414-22. PubMed ID: 25625937 [TBL] [Abstract][Full Text] [Related]
11. Markov state models from hierarchical density-based assignment. Mitxelena I; López X; de Sancho D J Chem Phys; 2021 Aug; 155(5):054102. PubMed ID: 34364321 [TBL] [Abstract][Full Text] [Related]
12. Motion of a disordered polypeptide chain as studied by paramagnetic relaxation enhancements, 15N relaxation, and molecular dynamics simulations: how fast is segmental diffusion in denatured ubiquitin? Xue Y; Skrynnikov NR J Am Chem Soc; 2011 Sep; 133(37):14614-28. PubMed ID: 21819149 [TBL] [Abstract][Full Text] [Related]
13. Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation. Moritsugu K; Koike R; Yamada K; Kato H; Kidera A PLoS One; 2015; 10(7):e0131583. PubMed ID: 26148295 [TBL] [Abstract][Full Text] [Related]
14. Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. Yasuda T; Shigeta Y; Harada R J Chem Inf Model; 2020 Aug; 60(8):4021-4029. PubMed ID: 32786508 [TBL] [Abstract][Full Text] [Related]
15. JEDi: java essential dynamics inspector - a molecular trajectory analysis toolkit. David CC; Avery CS; Jacobs DJ BMC Bioinformatics; 2021 May; 22(1):226. PubMed ID: 33932974 [TBL] [Abstract][Full Text] [Related]
16. Variance of Atomic Coordinates as a Dynamical Metric to Distinguish Proteins and Protein-Protein Interactions in Molecular Dynamics Simulations. Paul S; Ainavarapu SRK; Venkatramani R J Phys Chem B; 2020 May; 124(21):4247-4262. PubMed ID: 32281802 [TBL] [Abstract][Full Text] [Related]
17. From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models. Kabir KL; Akhter N; Shehu A J Bioinform Comput Biol; 2019 Dec; 17(6):1940014. PubMed ID: 32019409 [TBL] [Abstract][Full Text] [Related]
18. Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature. Mitsutake A; Takano H J Chem Phys; 2015 Sep; 143(12):124111. PubMed ID: 26429000 [TBL] [Abstract][Full Text] [Related]
19. In silico elucidation of the recognition dynamics of ubiquitin. Long D; Brüschweiler R PLoS Comput Biol; 2011 Apr; 7(4):e1002035. PubMed ID: 21533067 [TBL] [Abstract][Full Text] [Related]
20. Using robotics to fold proteins and dock ligands. Brutlag D; Apaydin S; Guestrin C; Hsu D; Varma C; Singh A; Latombe JC Bioinformatics; 2002; 18 Suppl 2():S74. PubMed ID: 12385986 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]