The DynaMine webserver: Predicting protein dynamics from sequence

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Cilia, Elisa ^a,b   Pancsa, Rita ^c,d   Tompa, Peter ^b,c,d,e   Lenaerts, Tom ^a,b,c   Vranken, Wim F ^b,c,d  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b Interuniversity Institute of Bioinformatics in Brussels (IB)2   (Belgium)

^c VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^d DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^e INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CLIENT SERVER APPLICATION; COMPUTER PREDICTION; COMPUTER SYSTEM; DYNAMINE; MOLECULAR DYNAMICS; ONLINE SYSTEM; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; SEQUENCE ANALYSIS; VALIDATION PROCESS; WEB BROWSER;

INTERNET; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

DYNAMINE;

EID: 84904815090     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku270     Document Type: Article

References (26)

1. Teilum,K., Olsen,J.G. and Kragelund,B.B. (2009) Functional aspects of protein flexibility. Cell. Mol. Life Sci., 66, 2231-2247.
2. Tompa,P. (2002) Intrinsically unstructured proteins. Trends Biochem. Sci., 27, 527-533.
3. Uversky,V.N. (2009) Intrinsic disorder in proteins associated with neurodegenerative diseases. Front. Biosci., 14, 5188-5238.
4. Dyson,H.J. andWright,P.E. (2005) Intrinsically unstructured proteins and their functions.Nat. Rev. Mol. Cell Biol., 6, 197-208.
5. Wright,P.E. and Dyson,H.J. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol., 293, 321-331.
6. Schweitzer-Stenner,R. (2012) Conformational propensities and residual structures in unfolded peptides and proteins. Mol. BioSyst., 8, 122-133.
7. Liang,S., Li,L., Hsu,W.-L., Pilcher,M.N., Uversky,V., Zhou,Y., Dunker,A.K. and Meroueh,S.O. (2009) Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry, 48, 399-414.
8. de Brevern,A.G., Bornot,A., Craveur,P., Etchebest,C. and Gelly,J.C. (2012) PredyFlexy: flexibility and local structure prediction from sequence. Nucleic Acids Res., 40, W317-W322.
9. Lange,O.F., Lakomek,N.-A., Farès,C., Schröder,G.F., Walter,K.F.A., Becker,S., Meiler,J., Grubmüller,H., Griesinger,C. and de Groot,B.L. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science, 320, 1471-1475.
10. Berjanskii,M.V. and Wishart,D.S. (2008) Application of the random coil index to studying protein flexibility. J. Biomol. NMR, 40, 31-48.
11. Ulrich,E., Akutsu,H., Doreleijers,J., Harano,Y., Ioannidis,Y.E., Lin,J., Livny,M., Mading,S., Maziuk,D., Miller,Z. et al. (2008) BioMagResBank. Nucleic Acids Res., 36, D402-D408.
12. Cilia,E., Pancsa,R., Tompa,P., Lenaerts,T. and Vranken,W.F. (2013) From protein sequence to dynamics and disorder with DynaMine. Nat. Commun., 4:2741, 1-10.
13. Zhang,F. and Brüschweiler,R. (2002) Contact model for the prediction of NMR N-H order parameters in globular proteins. J. Am. Chem. Soc., 124, 12654-12655.
14. Trott,O., Siggers,K., Rost,B. and Palmer,A.G. 3rd. (2008) Protein conformational flexibility prediction using machine learning. J. Magn. Reson., 192, 37-47.
15. Dosztanyi,Z., Csizmok,V., Tompa,P. and Simon,I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
16. Ishida,T. and Kinoshita,K. (2007) PrDOS: prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res., 35, W460-W464.
17. Walsh,I., Martin,A.J., Di Domenico,T. and Tosatto,S.C. (2012) ESpritz: accurate and fast prediction of protein disorder. Bioinformatics, 28, 503-509.
18. Daughdrill,G.W., Borcherds,W.M. and Wu,H. (2011) Disorder predictors also predict backbone dynamics for a family of disordered proteins. PloS One, 6, e29207.
19. Dyson,H.J. (2011) Expanding the proteome: disordered and alternatively folded proteins. Q. Rev. Biophys., 44, 467-518.
20. Berjanskii,M.V. and Wishart,D.S. (2007) The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res., 35, W531-W537.
21. Heinig,M. and Frishman,D. (2004) STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res., 32, W500-W502.
22. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
23. Joosten,R.P., te Beek,T.A., Krieger,E., Hekkelman,M.L., Hooft,R.W., Schneider,R., Sander,C. and Vriend,G. (2011) A series of PDB related databases for everyday needs. Nucleic Acids Res., 39, D411-D419.
24. UniProt,C. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
25. 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.
26. Oates,M.E., Romero,P., Ishida,T., Ghalwash,M.,Mizianty,M.J., Xue,B., Dosztanyi,Z., Uversky,V.N., Obradovic,Z., Kurgan,L. et al. (2013) D(2)P(2): database of disordered protein predictions. Nucleic Acids Res., 41, D508-D516.