This page is also available in: 日本語

eF-site

eF-site a database for molecular surfaces of proteins' functional sites

eF-site(electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms.

URL: http://pdbj.org/efsite/

eF-surf

eF-surf calculate the molecular surface

eF-surfis a web server to calculate the molecular surface of the up-loaded file with PDB format in the same way as the eF-site database.

URL: http://pdbj.org/efsurf/

eF-seek

eF-seek search for the similar ligand binding sites

eF-seekis a web server to search for the similar ligand binding sites for the uploaded coordinate file with PDB format. The representative binding sites in eF-site database are search by our own algorithm based on the clique search algorithm.

URL: http://pdbj.org/efseek/

ProMode Elastic

ProMode Elastic a database of normal mode analysis of PDB data

ProMode Elasticis 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).

URL: /promode-elastic/

hGTOP

hGTOP a database containing annotations of proteins in human, mouse and rat genomes

hGTOP is a database containing annotations of proteins in human, mouse and rat genomes. The annotations are mainly about homologous proteins with known 3D structures as well as other structural information such as predicted (or observed) secondary structures and disordered regions. In addition, for each protein in the above genomes, homologous proteins in the genomes of approximately 170 representative organisms are listed.

URL: http://p4d-info.nig.ac.jp/hGTOP/

2012-07-11 (last edited: 4 months ago)2016-04-01
PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan