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Thornton Group Services and DatabasesMost of the following services are maintained by members of the Thornton Group at the EBI. Others are links to services maintained by collaborators or to databases developed during the Thornton Group's time at UCL.
Services hosted at the EBICatalytic Site AtlasThe 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.
Cofactor databaseThis database is a collection of primary literature knowledge and mechanisms of organic enzyme cofactors. It integrates information on organic enzyme cofactors with various compound and enzyme resources. The purpose of CoFactor is to gather information about cofactors in order to learn about the role of organic enzyme cofactors in biocatalysis.
ENTRAPExon/Intron Annotation of Proteins (ENTRAP) is a resource for annotating protein chains of known structure with intron and exon data.
Enzyme Structures DatabaseThis database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB). There are currently 13,582 PDB-enzyme entries in the PDB (as at 15 October, 2004) involving 12,967 separate PDB files - some files having more than one E.C. number associated with them.
FunTreeFunTree is a resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. It allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme's sequence and structure but also the relationships of their reactions. It is developed in tandem with the CATH database at UCL.
MACiEMACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project between the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute. MACiE currently contains 202 fully annotated enzyme reaction mechanisms, which comprise 199 EC numbers (158 EC sub-subclasses) and 285 distinct CATH codes.
PDBsumPDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank. It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D.
PitaPita is a program which tries to suggest the most likely biological unit for a given X-ray crystal structure of a protein based on the crystal symmetry operators and a method of scoring each trial protein-protein interface.PoreLogoPoreLogo is an automated tool for the visualization of sequence and conservation of pore-lining residues in transmembrane protein structuresPoreWalkerPoreWalker is a fully automated method designed to detect and characterise transmembrane protein channels from their 3D structure.PROCOGNATEPROCOGNATE is a database of cognate ligands for the domains of enzymes in the SCOP and CATH protein classifications.
ProFuncThe ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods to try to provide clues as the the protein's likely or possible function. Often, where one method fails to provide any functional insight another may be more helpful.
SASSAS is a sequence search program that uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank. The resultant multiple alignment can be coloured according to different structural features. The matching 3D structures can be superimposed and viewed in RasMol.
ScoreconsScorecons is a program that quantifies residue conservation in a multiple sequence alignment. Given a multiple sequence alignment file, Scorecons calculates the degree of amino acid variability in each column of the alignment and returns this information to the user.ScoreconsScorecons is a program that quantifies residue conservation in a multiple sequence alignment. Given a multiple sequence alignment file, Scorecons calculates the degree of amino acid variability in each column of the alignment and returns this information to the user.Services hosted at UCL
Atlas of Protein Side-Chain InteractionsThis atlas depicts how amino acid side-chains pack against one another within the known protein structures. This packing, which is governed by the interactions between the 20 different types of side-chains, determines the structure, function, and stability of proteins.Protein-DNA InteractionsThe supplementary web page for Luscombe et al (2000). An overview of the structures of protein-DNA complexes. Genome Biology 1:1-37.Protein-Nucleic Acid Interaction ServerThis server is a tool to analyse the protein interface of any protein-nucleic acid complex. You can submit the coordinates of a complex of your choice and then view tables describing the nature of the interface.TempuraTempura is a function prediction tool and local structural comparison service. It uses the "reverse template" approach published as part of the ProFunc server but has been modified to allow the user to specify the amino acids to be used in the template generation process.Affiliated services
CATHCATH is a novel hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H). Class, derived from secondary structure content, is assigned for more than 90% of protein structures automatically. Architecture, which describes the gross orientation of secondary structures, independent of connectivities, is currently assigned manually. The topology level clusters structures according to their toplogical connections and numbers of secondary structures. The homologous superfamilies cluster proteins with highly similar structures and functions. The assignments of structures to toplogy families and homologous superfamilies are made by sequence and structure comparisons.ContactWe would like to encourage laboratories wishing to discuss any collaborations to contact us. For information, comments and/or suggestions please contact us. |
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