TUAT Kuroda Lab.

IS-Dom

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ISD Checker
-- Asseses the independence of a proposed domain in a PDB chain.
PDB ID_Chain* ** Region # -
Input PDB ID (List), Chain ID and Residue number (#Start - End) corresponding to the PDB file. ( example: 1tqc_C 1-113 )


ISD Generator
-- Generate an ISD dataset using user's setting.
Domain Definition
SCOP CATH
DP* All
Select a domain database from
which ISDs are derived .
*DP:DomainParser
Hydrogen Bond MC<-->MC Threshold number of inter-domain Hbonds
calculated by HBPLUS( I.K.McDonald,et al. )

MC=MainChain ,SC=SideChain
MC<-->SC
SC<-->SC
Hydrophobic Cluster
Distance: A 		Select distance threshold and threshold number of HPC.
HPC is assumed when distance between 3 hydrophobic residue
are within a distance threshold. calculated from PDB coordinates

IS-Dom is the domain database created by Kuroda lab.
Our new method refined the definition of "structural domain" as given in
various domain dataset,and selected proteins with autonomouly foldable domains.

Last modification: Nov. 2013

Teppei Ebina, Yuki Umezawa, Yutaka Kuroda:
IS-Dom: a dataset of independent structural domains automatically delineated from protein structures.
J Comput Aided Mol Des. 2013 May;27(5):419-26.
Copyright (c) 2011 TUAT Kuroda Lab All Rights Reserved.