Improvements in ProMode (a Database of Normal Mode Analyses of Proteins)
نویسندگان
چکیده
ProMode (http://promode.socs.waseda.ac.jp/) is a database collecting the results from normal mode analyses (NMA) of various protein molecules [3]. Although NMA is based on the harmonic approximation, it has been shown by many studies that the results from NMA are not only reasonable qualitatively in most cases, but also can provide a proper description of the functionally important motions of the protein. The collection of the NMA results for various proteins is useful for comparative and statistical studies of the dynamic structures of proteins. For further details of the method of NMA and the contents of ProMode, see the reference 3.
منابع مشابه
ProMode-Oligomer: Database of Normal Mode Analysis in Dihedral Angle Space for a Full-Atom System of Oligomeric Proteins
The database ProMode-Oligomer (http://promode.socs.waseda.ac.jp/promode_oligomer) was constructed by collecting normal-mode-analysis (NMA) results for oligomeric proteins including protein-protein complexes. As in the ProMode database developed earlier for monomers and individual subunits of oligomers (Bioinformatics vol. 20, pp. 2035–2043, 2004), NMA was performed for a full-atom system using ...
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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...
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1 School of Social Sciences, Waseda University, 1-6-1, Nishi-Waseda, Shinjuku-ku, Tokyo 169-8050, Japan 2 NEC Soft, Ltd., 1-18-7, Shinkiba, Koto-ku, Tokyo 136-8627, Japan 3 Sciencehouse, Inc., 1-4-17, Higashi-Tabata, Kita-ku, Tokyo 114-0013, Japan 4 Department of Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, 1-7-29, Suehiro-cho, T...
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