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Promode Elastic

Database of normal mode analysis of PDB data using elastic network model in torsional angle space

ProMode-Elastic is a database of normal mode analysis of PDB data. The normal mode analysis is performed by the program PDBETA we have developed. PDBETA is a program of Elastic-network-model based normal mode analysis in Torsional Angle space for PDB data. PDBETA can describe molecular structures with relatively smaller number of degrees of freedom, and take into computation not only proteins but also DNA, RNA, and ligand molecules (hydrogen atoms and water molecules are excluded currently to suppress the number of variables).

In each protein page its characteristic dynamic features can be observed through animation and displacement vectors on a viewer such as jV and Jmol. We hope that a user learns more about dynamics from these pages than a static three-dimensional structure image of PDB data.

Reference
No. of entries
PDB:64890
Chain:86301
Total:151191
  • Hiroshi Wako and Shigeru Endo, "Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables." Comp. Biol. Chem. Vol. 44, 22-30 (2013) [doi:10.1016/j.compbiolchem.2013.02.006]
  • Hiroshi Wako and Shigeru Endo, "Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis." Biophys. Chem. Vol. 159, 257-266 (2011) [doi:10.1016/j.bpc.2011.07.004]


Topics:
14/5/2012 ProMode-Elastic server has been moved to PDBj, IPR, Osaka University. URL was also changed.
9/10/2010 ProMode-Elastic first version is released.
12/12/2009 ProMode-Elastic test version is released.


Download PDBeta.


PDB code (4 chars, e.g. 1a00):




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