FN Thomson Reuters Web of Science™
VR 1.0
PT J
AU Bakan, A
   Meireles, LM
   Bahar, I
AF Bakan, Ahmet
   Meireles, Lidio M.
   Bahar, Ivet
TI ProDy: Protein Dynamics Inferred from Theory and Experiments
SO BIOINFORMATICS
LA English
DT Article
ID PRINCIPAL COMPONENT ANALYSIS; INTRINSIC DYNAMICS; MOLECULAR-DYNAMICS;
   DEFORMATION; SUPERFAMILY; FLEXIBILITY; ENZYMES; MOTIONS; MODES
AB We developed a Python package, ProDy, for structure-based analysis of protein dynamics. ProDy allows for quantitative characterization of structural variations in heterogeneous datasets of structures experimentally resolved for a given biomolecular system, and for comparison of these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence of their substrates, ligands or inhibitors. Numerous helper functions enable comparative analysis of experimental and theoretical data, and visualization of the principal changes in conformations that are accessible in different functional states. ProDy application programming interface (API) has been designed so that users can easily extend the software and implement new methods.
C1 [Bakan, Ahmet] Univ Pittsburgh, Dept Computat & Syst Biol, Sch Med, Pittsburgh, PA 15213 USA.
   Univ Pittsburgh, Clin & Translat Sci Inst, Sch Med, Pittsburgh, PA 15213 USA.
RP Bakan, A (reprint author), Univ Pittsburgh, Dept Computat & Syst Biol, Sch Med, 3064 BST3,3501 5th Ave, Pittsburgh, PA 15213 USA.
EM ahb12@pitt.edu; bahar@pitt.edu
FU National Institutes of Health [1R01GM086238-01, UL1 RR024153]
FX National Institutes of Health (1R01GM086238-01 to I.B. and UL1 RR024153
   to A.B.).
NR 21
TC 137
Z9 138
U1 3
U2 31
PU OXFORD UNIV PRESS
PI OXFORD
PA GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND
SN 1367-4803
J9 BIOINFORMATICS
JI Bioinformatics
PD JUN 1
PY 2011
VL 27
IS 11
BP 1575
EP 1577
DI 10.1093/bioinformatics/btr168
PG 3
WC Biochemical Research Methods; Biotechnology & Applied Microbiology;
   Computer Science, Interdisciplinary Applications; Mathematical &
   Computational Biology; Statistics & Probability
SC Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology;
   Computer Science; Mathematical & Computational Biology; Mathematics
GA 770BQ
UT WOS:000291062400020
PM 21471012
ER

EF