Sites & Motifs
The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.
http://www.ebi.ac.uk/thornton-srv/databases/CSA/
SuMo allows you to screen the Protein Data Bank (PDB) for finding ligand binding sites matching your protein structure or inversely, for finding protein structures matching a given site in your protein. This method is neither based on aminoacid sequence nor on fold comparisons.
http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome
All structures are reduced to matrices that contain just enough information to define a fold, so the definition is general and large deviations in coordinates are tolerated. A user supplies a matrix for a motif, and ProSMoS lists all structures that exactly match this motif.
http://prodata.swmed.edu/ProSMoS/
Multiple alignment of protein binding sites recognizes spatial chemical binding patterns common to a Set of protein Structures.
http://bioinfo3d.cs.tau.ac.il/MultiBind/
SiteEngine recognizes regions on the surface of one protein that resemble a specific binding site of another.
http://bioinfo3d.cs.tau.ac.il/SiteEngine/
Patterns In Non-homologous Tertiary Structures. PINTS finds similarities between protein structures consisting of amino acids that are close in space, but not necessarily close or co-linear in sequence (local structural patterns, for example the catalytic triad). Unlike other tools, PINTS does not aim to find proteins adopting a similar fold.
http://www.russell.embl.de/pints/
FunClust is a web server for the identification of local functional motifs in a set of non homologous protein structures
http://pdbfun.uniroma2.it/funclust/help.py
The LabelHash suite of programs and scripts can be used to match point-based structural motifs to a set of target proteins. A motif is defined by the C-alpha positions of a number of residues. Associated with each motif point is a number of allowed residue labels.
http://kavrakilab.org/labelhash/labelhash.html
RASMOT-3D PRO searches in protein structure files for proteins possessing a group of residues in a topology similar to that adopted by a 3D motif given in input.
http://biodev.extra.cea.fr/rasmot3d/
Given a set of motifs and a reference sequence, seeMotif helps to visualize and exploring these motifs in appropriate structures selected based on a reference sequence.
http://seemotif.csie.ntu.edu.tw/index.html
ProtMot, a PROTeins MOTif analysis tool. This web site analyzes structure of proteins and output the list of hydrogen bonding patterns network motifs. The list of motifs, a superset of the secondary structures, is shown both projected on the protein structure and as a network motif significance profile (SP), a chart which gives the occurrences of each motif in the protein.
http://bioinfo.weizmann.ac.il/protmot/
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