Bioinformatics Links Directory : Domains and MotifsThis section includes links to tools which can give information about protein domains and/or predict motifs, domains, and patterns in peptide sequences.FoldMiner and LOCK 2- (Found July 8, 2008 ) FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.http://foldminer.stanford.edu/ FISH- (Found July 8, 2008 ) Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.http://max.ucmp.umu.se/sahmm/ FF - Fragment Finder- (Found July 8, 2008 ) FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against.http://cluster.physics.iisc.ernet.in/ff/ fastSCOP- (Found July 8, 2008 ) fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.http://gemdock.life.nctu.edu.tw/fastSCOP/ 3dLOGO- (Found July 8, 2008 ) 3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.http://3dlogo.uniroma2.it/3dLOGO/home.html |