TY - JOUR
KW - Kinetics
KW - Models, Molecular
KW - Peptides
KW - Thermodynamics
KW - Animals
KW - Algorithms
KW - Molecular Structure
KW - Proteins
KW - Surface Properties
KW - Software
KW - Vibration
AU - M. Seeber
AU - A. Felline
AU - F. Raimondi
AU - S. Muff
AU - R. Friedman
AU - F. Rao
AU - A. Caflisch
AU - F. Fanelli
AB - <p>Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra-molecular and inter-molecular communication paths, kinetic grouping analysis, and calculation of mincut-based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net.</p>
BT - Journal of Computational Chemistry
C1 - 0143
DA - 2011 Apr 30
DO - 10.1002/jcc.21688
IS - 6
J2 - J. Comput. Chem.
LA - eng
M3 - Research Article
N2 - <p>Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra-molecular and inter-molecular communication paths, kinetic grouping analysis, and calculation of mincut-based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net.</p>
PY - 2011
SP - 1183
EP - 1194
T2 - Journal of Computational Chemistry
TI - Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
VL - 32
SN - 1096-987X
ER -