Conformational dynamics data bank: A database for conformational dynamics of proteins and supramolecular protein assemblies

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Kim, Do Nyun ^a   Altschuler, Josiah ^b   Strong, Campbell ^b   McGill, Gaël ^b,c   Bathe, Mark ^a  

^a Massachusetts Institute of Technology   (United States)

^b Digizyme Inc   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERISM; ARTICLE; AUTOMATION; CONFORMATIONAL DYNAMICS DATA BANK; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MOLECULAR WEIGHT; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE;

DATABASES, PROTEIN; MULTIPROTEIN COMPLEXES; PROTEIN CONFORMATION; PROTEINS; USER-COMPUTER INTERFACE;

EID: 78651266383     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1088     Document Type: Article

References (37)

1. Ma,J.P. and Karplus,M. (1998) The allosteric mechanism of the chaperonin GroEL: A dynamic analysis. Proc. Natl Acad. Sci. USA,95,8502-8507.
2. Cui,Q. and Karplus,M. (2008) Allostery and cooperativity revisited. Protein Sci.,17,1295-1307.
3. Kern,D. and Zuiderweg,E.R.P. (2003) The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol.,13,748.
4. Csermely,P.,Palotai,R. and Nussinov,R. (2010) Induced fit,conformational selection and independent dynamic segments: An extended view of binding events. Trends Biochem. Sci.,35,539-546.
5. Zheng,W.J.,Brooks,B.R. and Thirumalai,D. (2006) Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc. Natl Acad. Sci. USA,103,7664-7669.
6. Tagari,M.,Newman,R.,Chagoyen,M.,Carazo,J.M. and Henrick,K. (2002) New electron microscopy database and deposition system. Trends Biochem. Sci.,27,589.
7. Henrick,K.,Newman,R.,Tagari,M. and Chagoyen,M. (2003) EMDep: A web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. J. Struct. Biol.,144,228-237.
8. Bernstein,F.C.,Koetzle,T.F.,Williams,G.J.B.,Meyer,E.F.,Brice,M.D., Rodgers,J.R.,Kennard,O.,Shimanouchi,T. and Tasumi,M. (1977) The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol.,112,535-542.
9. Berman,H.M.,Westbrook,J.,Feng,Z.,Gilliland,G.,Bhat,T.N.,Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The protein data bank. Nucleic Acids Res.,28,235-242.
10. Alexandrov,V.,Lehnert,U.,Echols,N.,Milburn,D.,Engelman,D. and Gerstein,M. (2005) Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool. Protein Sci.,14,633-643.
11. Suhre,K. and Sanejouand,Y.-H. (2004) ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res.,32,W610-W614.
12. Wako,H.,Kato,M. and Endo,S. (2004) ProMode: A database of normal mode analyses on protein molecules with a full-Atom model. Bioinformatics,20,2035- 2043.
13. Yang,L.W.,Liu,X.,Jursa,C.J.,Holliman,M.,Rader,A.,Karimi,H.A. and Bahar,I. (2005) iGNM: A database of protein functional motions based on Gaussian network model. Bioinformatics,21,2978-2987.
14. Hollup,S.M.,Salensminde,G. and Reuter,N. (2005) WEBnm@: A web application for normal mode analyses of proteins. BMC Bioinformatics,6,52.
15. Lindahl,E.,Azuara,C.,Koehl,P. and Delarue,M. (2006) NOMAD-Ref: Visualization,deformation and refinement of macromolecular structures based on all-Atom normal mode analysis. Nucleic Acids Res.,34,W52-W56.
16. Cui,Q. and Bahar,I. (eds),(2006) Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Chapman & Hall/CRC,Boca Raton.
17. Brooks,B. and Karplus,M. (1985) Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme. Proc. Natl Acad. Sci. USA.,82,4995-4999.
18. Levitt,M.,Sander,C. and Stern,P.S. (1985) Protein normal-mode dynamics: Trypsin inhibitor,crambin,ribonuclease and lysozyme. J. Mol. Biol.,181,423-447.
19. Zheng,W.J.,Brooks,B.R.,Doniach,S. and Thirumalai,D. (2005) Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure,13,565-577.
20. Maragakis,P. and Karplus,M. (2005) Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J. Mol. Biol.,352,807-822.
21. Miyashita,O.,Onuchic,J.N. and Wolynes,P.G. (2003) Nonlinear elasticity,proteinquakes,and the energy landscapes of functional transitions in proteins. Proc. Natl Acad. Sci. USA.,100,12570-12575.
22. Brink,J.,Ludtke,S.J.,Kong,Y.F.,Wakil,S.J.,Ma,J.P. and Chiu,W. (2004) Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure,12,185-191.
23. Brooks,B.R.,Bruccoleri,R.E.,Olafson,B.D.,States,D.J.,Swaminathan,S. and Karplus,M. (1983) CHARMM-A program for macromolecular energy,minimization,and dynamics calculations. J. Comput. Chem.,4,187-217.
24. Go,N.,Noguti,T. and Nishikawa,T. (1983) Dynamics of a small globular protein in terms of low frequency vibrational modes. Proc. Natl Acad. Sci. USA.,80,3696-3700.
25. Bathe,M. (2008) A finite element framework for computation of protein normal modes and mechanical response. Proteins: Struct. Funct. Bioinform.,70,1595-1609.
26. Kim,D.-N.,Nguyen,C.-T. and Bathe,M. (2010) Conformational dynamics of supramolecular protein assemblies. J. Struct. Biol. (in press).
27. Shepherd,C.M.,Borelli,I.A.,Lander,G.,Natarajan,P.,Siddavanahalli,V., Bajaj,C.,Johnson,J.E.,Brooks,C.L. and Reddy,V.S. (2006) VIPERdb: A relational database for structural virology. Nucleic Acids Res.,34,D386-D389.
28. Carrillo-Tripp,M.,Shepherd,C.M.,Borelli,I.A.,Venkataraman,S.,Lander,G., Natarajan,P.,Johnson,J.E.,Brooks,C.L. III and Reddy,V.S. (2009) VIPERdb2: An enhanced and web API enabled relational database for structural virology. Nucleic Acids Res.,37,D436-D442.
29. Lorensen,W.E. and Cline,H.E. (1987) Marching cubes: A high resolution 3D surface construction algorithm. Computer Graphics (SIGGRAPH '87 Proceedings),21,163-169.
30. Pettersen,E.F.,Goddard,T.D.,Huang,C.C.,Couch,G.S.,Greenblatt,D.M.,Meng,E. C. and Ferrin,T.E. (2004) UCSF Chimera-A visualization system for exploratory research and analysis. J. Comput. Chem.,25,1605-1612.
31. Cignoni,P.,Callieri,M.,Corsini,M.,Dellepiane,M.,Ganovelli,F. and Ranzuglia,G. (2008) Sixth Eurographics Italian Chapter Conference,pp. 129-136.
32. McQuarrie,D.A. (1975) Statistical Mechanics. Harper & Row,New York.
33. Lange,O.F. and Grubmüller,H. (2006) Generalized correlation for biomolecular dynamics. Proteins: Struct. Funct. Bioinform.,62,1053-1061.
34. Sedeh,R.S.,Fedorov,A.A.,Fedorov,E.V.,Ono,S.,Matsumura,F.,Almo,S.C. and Bathe,M. (2010) Structure,evolutionary conservation,and conformational dynamics of Homo sapiens fascin-1,an F-Actin crosslinking protein. J. Mol. Biol.,400,589-604.
35. Gibbons,M.M. and Klug,W.S. (2007) Nonlinear finite-element analysis of nanoindentation of viral capsids. Phys. Rev. E.,75,031901.
36. Gibbons,M.M. and Klug,W.S. (2008) Influence of nonuniform geometry on nanoindentation of viral capsids. Biophys. J.,95,3640-3649.
37. Ludtke,S.J.,Jakana,J.,Song,J.-L.,Chuang,D.T. and Chiu,W. (2001) A 11.5Å single particle reconstruction of GroEL using EMAN. J. Mol. Biol.,314,253-262.