From Proteinfunction.net

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Contents 1 ArchDB 2 BLOCKS 3 BRENDA 4 CASTp 5 Catalytic Sites Atlas 6 eF-site 7 ELISA 8 LigBase 9 PDB-UF 10 PRINTS 11 Prosite 12 SCOPEC 13 SitesBase

ArchDB

• A compilation of structural classification of loops extracted from known protein structures.
• Protein loop regions can be used because they play crucial roles in a protein's function.

BLOCKS

• http://www.psc.edu/general/software/packages/blocks/blocks.html
• Database of multiple motifs, typically ~20 residues long, presented in the form of ungapped multiple sequence alignments.

BRENDA

• http://www.brenda.uni-koeln.de/together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms.

CASTp

• http://sts.bioengr.uic.edu/castp/index.php
• Binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities. castP server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules. It measures analytically the area and volume of each pocket and cavity, both in solvent accessible surface (SA, Richards' surface) and molecular surface (MS, Connolly's surface). It also measures the number of mouth openings, area of the openings, circumference of mouth lips, in both SA and MS surfaces for each pocket.

Catalytic Sites Atlas

• http://www.ebi.ac.uk/thornton-srv/databases/CSA/

• The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. They 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.

eF-site

• http://ef-site.hgc.jp/eF-site/
• eFsite (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties

ELISA

• http://romi.bu.edu/elisa/
• Database of function annotation based on sequence-structure neighborhoods defined from PDUG ( Protein domain universe graph) which is constructed by structure comparison of template proteins.

LigBase

• http://alto.compbio.ucsf.edu/ligbase/
• This is a database of ligand binding proteins aligned to structural templates.

PDB-UF

• http://paradox.harvard.edu/PDB-UF/
• Database of predicted enzyme function for proteins without function annotation deposited in PDB. Structure comparison and clustering method are combined for this.

PRINTS

• http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/
• Same concept with BLOCKS database, but it includes biological documentation of the significance of the motifs.

Prosite

• Database of protein domains, families, and functional sites.
• The proteins doing the same function(s) are done MSA(Multiple Sequence Alignment), then shared functional sites(motif) are located. These sites are expressed by regular expressions or a profile

SCOPEC

• http://www.enzome.com/enzome/databases/scopec.php
• SCOPEC defines EC numbers for each scop domain.
  
• Helpful for domain based protein function prediction.

SitesBase

• http://www.modelling.leeds.ac.uk/sb/
• SitesBase is a database of known ligand binding sites within the PDB which is navigable by PDB identifier or ligand 3 letter code e.g. NAD. Each binding site has a frequently updated register of structurally similar binding sites sharing atomic similarity detected by geometric hashing (Brakoulias and Jackson 2004). Multiple alignments, structural superpositions and links to other structural databases are also available enabling further analysis.