PiSQRD: A web server for decomposing proteins into quasi-rigid dynamical domains

Bioinformatics

Volumn 25, Issue 20, 2009, Pages 2743-2744

  Aleksiev, T ^a   Potestio, R ^a   Pontiggia, F ^a   Cozzini, S ^a,b   Micheletti, C ^a,b,c  

^a SISSA   (Italy)

^b DEMOCRITOS NATIONAL SIMULATION CENTER   (Italy)

^c ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID DERIVATIVE; PROTEIN DERIVATIVE;

ARTICLE; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DECOMPOSITION; INTERNET; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; DATABASES, PROTEIN; INTERNET; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 70349978984     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp512     Document Type: Article

References (9)

1. Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
2. Garcia,A. (1992) Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett., 68, 2696-2699.
3. Hayward,S. et al. (1997) Model-free methods of analyzing domain motions in proteins from simulation. Proteins Struct. Funct. Genet. 27, 425-437.
4. Hinsen,K. (2000) The molecular modeling toolkit, J. Comput. Chem., 21, 79-85.
5. Micheletti,C. et al. (2004) Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models. Proteins, 55, 635-645.
6. Painter,J. and Merritt,E.A. (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Cryst., D62, 439-450.
7. Potestio,R. et al. (2009) Coarse-grained description of proteins' internal dynamics: An optimal strategy for decomposing proteins in rigid subunits. Biophys. J., 96, 4993-5002.
8. Schomaker,V. and Trueblood,K.N. (1968) On rigid-body motion of molecules in crystals. Acta Cryst., B24, 63-76.
9. Wako,H. et al. (2004) ProMode: A database of normal mode analyses on protein molecules with a full-atom model. Bioinformatics, 20 2035-2043.