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COMBREX-DB / COMputational BRidges to EXperiments DataBase
Provides information about experimentally determined protein function, relationships among proteins of unknown function and various types of experimental data. COMBREX-DB contains information on approximately 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. It can help users to identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The database is searchable by gene names, descriptions, predictions, and identifiers.
FunTree
A resource that brings together protein sequence, structure and functional information, including overall chemical reaction and mechanistic data, for structurally defined domain superfamilies. FunTree uses the CATH classification to annotate and analyse super families of enzymes. In particular the relationships between known 3 dimensional structures, associated sequences and the enzyme chemistry is highlighted. This can be used to place structures and sequences in context of their evolution and the range and similarities/differences in the reaction chemistry (both bond order changes and small molecule substructure). In addition it can be used to infer the possible range of reactions of enzyme structures and sequences that do not have a known function as well as indicating other reactions or substrates available to an enzyme that as yet may not have been observed (enzyme promiscuity).
KIDFamMap / Kinase-inhibitor-disease family map
Allows exploration of kinase-inhibitor families (KIFs) and kinase-inhibitor-disease (KID) relationships. KIDFamMap can provide further insights in the elucidation of protein kinase inhibitor selectivity and binding mechanisms. It can be used to design selective kinase inhibitors. The database contains about 1200 KIFs, 960 kinase-disease relationships, 187 000 kinase-inhibitor assays, 340 kinase-related diseases and 638 disease allelic variants.
SALAD / Surveyed conserved motif ALignment diagram and the Associating Dendrogram
Permits to elucidate the biological function of proteins. SALAD is a plant comparative genomics database that offers valuable information for plant researchers for the design of molecular biology experiments. This genome-wide database is based on a similarity clustering by original scoring of distribution patterns of evolutionarily conserved motifs for all possible sequence pairs in a high percent similarity protein group.
PA-GOSUB / Proteome Analyst: Gene Ontology molecular function and Subcellular Localization
Provides gene ontology (GO) and subcellular localization annotations. PA-GOSUB offers search and browsing capabilities that add query functionality to the pre-computed model organisms. It contains more than 140 000 proteins, about 27 000 Gene Ontology Annotation (GOA) and more than 100 000 Proteome Analyst (PA) for Gene Ontology (GO) molecular function. The database can be used to assist users to understand why a classifier makes a particular classification thank to the implementation of an explanation mechanism.
BASID2CS / The basidiomycetes Two Componen Systems repository
A pipeline web server that extends the analysis to the complete genome sequences of basidiomycetes. BASID2CS has been specifically designed for the identification, classification and functional annotation of putative TCS proteins from any predicted proteome. This pipeline is specifically designed and implemented for the bioinformatic screening and extraction of all the putative TCS proteins from each predicted proteome of basidiomycetes in a single step. All the TCS proteins in Agaricus remain to be characterized and the present genomic analysis paves the way for future TCS functional studies in this basidiomycete fungus.
SIMAP / Similarity Matrix of Proteins
Obsolete
A database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes. SIMAP provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories.
NRPS-PKS
Obsolete
Permits comparison of Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) domains. NRPS-PKS is a knowledge-based tool for analysing putative NRPS and PKS gene clusters. It uses a knowledge-based approach for prediction of domain organization and substrate specificity. This method facilitates easy extraction from a polypeptide sequence of various domains and identification of their catalytic activity, active site residues, and substrate specificity.
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