Domain Prediction, Globularity and Assembly Analysis
pDomain resource is centered around defining structural domains from 3D coordinates. This resource brings together current state-of-the-art algorithmic methods for partitioning proteins into domains.
http://pdomains.sdsc.edu/v2/index.php
Search for Conserved Domains within a protein sequence.
http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
Dompred is a server designed to predict putative protein domains and their boundaries for a given protein sequence. The server uses several methods, from identifying obvious similarities to Pfam-A domain sequences to predicting domains using DomSSEA in cases where sequence searching has yielded no results.
http://bioinf.cs.ucl.ac.uk/dompred/
The approach 'Protein Peeling' aims at cutting the 3D protein structure into a limited set of 'Protein Units'. A more precise definition of protein unit is a compact sub-region of the 3D structure corresponding to one sequence fragment.
http://www.dsimb.inserm.fr/dsimb_tools/peeling3/
DOMpro is a web server to predict protein domain boundaries using 1D-Recursive Neural Networks and statistical methods.
http://www.ics.uci.edu/~baldig/dompro.html
DIAL is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.
http://caps.ncbs.res.in/DIAL/home.html
PURE is a bioinformatics protocol to identify putative domains in the Unassigned Regions.
http://caps.ncbs.res.in/PURE/PURE.html
Domain 3D is a method developed by Willie Taylor to identify globular domains in protein structure.
http://www.ibi.vu.nl/programs/domain3Dwww/
DHcL (Domain Hierarchy and closed Loops)is a server for the analysis of basic structural units of a protein. The server calculates domain structures at different levels of energy hierarchy and elements of the loop-n-lock structure, closed loops and van derWaals locks.
http://sitron.bccs.uib.no/dhcl/
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