Bioinformatics Advance Access originally published online on April 1, 2004
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Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.
ProMode: a database of normal mode analyses on protein molecules with a full-atom model
1 School of Social Sciences, Waseda University, Tokyo 169-8050, Japan, 2 Department of Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan and 3 Department of Physics, School of Science, Kitasato University, Sagamihara 228-8555, Japan
Received on September 19, 2003; revised on February 10, 2004; accepted on February 27, 2004
Advance Access Publication April 1, 2004
Motivation: Although information from protein dynamics simulation is important to understand principles of architecture of a protein structure and its function, simulations such as molecular dynamics and Monte Carlo are very CPU-intensive. Although the ability of normal mode analysis (NMA) is limited because of the need for a harmonic approximation on which NMA is based, NMA is adequate to carry out routine analyses on many proteins to compute aspects of the collective motions essential to protein dynamics and function. Furthermore, it is hoped that realistic animations of the protein dynamics can be observed easily without expensive software and hardware, and that the dynamic properties for various proteins can be compared with each other.
Results: ProMode, a database collecting NMA results on protein molecules, was constructed. The NMA calculations are performed with a full-atom model, by using dihedral angles as independent variables, faster and more efficiently than the calculations using Cartesian coordinates. In ProMode, an animation of the normal mode vibration is played with a free plug-in, Chime (MDL Information Systems, Inc.). With the full-atom model, the realistic three-dimensional motions at an atomic level are displayed with Chime. The dynamic domains and their mutual screw motions defined from the NMA results are also displayed. Properties for each normal mode vibration and their time averages, e.g. fluctuations of atom positions, fluctuations of dihedral angles and correlations between the atomic motions, are also presented graphically for characterizing the collective motions in more detail.
Availability: http://promode.socs.waseda.ac.jp
Contact: wako{at}waseda.jp
* To whom correspondence should be addressed.
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