List of web resources for visualizing molecular dynamics Informatics 479 kategori-antropologi.pts-ptn.net

List of web resources for visualizing molecular dynamics

Name	License	Citation	Comments
ANM	free	^[1]	computes and visualizes normal modes
Ascalaph Graphics	free		visualizes MDynaMix simulations
Database of Macromolecular Movements	free	^[2]	analyzes protein hinge motions
Deneb	not free, TRIAL version available		Powerful Graphical User Interface for relevant DFT calculation packages (SIESTA, VASP, QE, etc.)
DSMM	free	^[3]	movies of MD simulations
Dynameomics	free	^[4]	interactive visualization of MD trajectories
FIRST/FRODA	free	^[5]	uses constraints to generate conformational ensembles and trajectories
Force Field Explorer	free		graphical interface to TINKER
MoDEL	free		deposit and access MD trajectories
Moviemaker	free	^[6]	generates animations of protein motions
NOMAD-ref	free	^[7]	compute and visualizes normal modes
VMD	free	^[8]	VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Yale Morph Server	free	^[2]	animations transitions between two states
YASARA	not free		fully featured molecular modeling and simulation program with interactive MD trajectory player

References

^ Eyal, E; et al., LW; Bahar, I (2006). "Anisotropic network model: systematic evaluation and a new web interface". Bioinformatics 22 (21): 2619–2627. doi:10.1093/bioinformatics/btl448. PMID 16928735.
^ ^a ^b Flores, S; et al., N; Milburn, D; Hespenheide, B; Keating, K; Lu, J; Wells, S; Yu, EZ et al. (2006). "The Database of Macromolecular Motions: new features added at the decade mark". Nucleic Acids Res 34 (Database issue): D296–D301. doi:10.1093/nar/gkj046. PMC 1347409. PMID 16381870. Citation uses old-style implicit et al. for authors
^ Finocchiaro, G; et al., T; Hoffmann, R; Gonzalez, A; Wade, RC (2003). "DSMM: a Database of Simulated Molecular Motions". Nucleic Acids Res 31 (1): 456–457. doi:10.1093/nar/gkg113. PMC 165560. PMID 12520051.
^ Kehl, C; et al., AM; Toofanny, RD; Daggett, V (2008). "Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data". Protein Eng Des Sel 21 (6): 379–386. doi:10.1093/protein/gzn015. PMID 18411222.
^ Thorpe, MF; et al., Ming; Rader, A.J.; Jacobs, Donald J.; Kuhn, Leslie A. (2001). "Protein flexibility and dynamics using constraint theory". J Mol Graph Model 19 (1): 60–69. doi:10.1016/S1093-3263(00)00122-4. PMID 11381531.
^ Maiti, R; et al., GH; Wishart, DS (2005). "MovieMaker: a web server for rapid rendering of protein motions and interactions". Nucleic Acids Res 33 (Web Server issue): W358–W362. doi:10.1093/nar/gki485. PMC 1160245. PMID 15980488.
^ Lindahl, E; et al., C; Koehl, P; Delarue, M (2006). "NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis". Nucleic Acids Res 34 (Web Server issue): W52–W56. doi:10.1093/nar/gkl082. PMC 1538881. PMID 16845062.
^ Humphrey, W; A. Dalke, K. Schulten (1996). "VMD - Visual Molecular Dynamics". J. Molec. Graphics 14: 33–38. doi:10.1016/0263-7855(96)00018-5. PMID 8744570.

List of web resources for visualizing molecular dynamics

See also

References