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).
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.
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.
Supplies contents and method to study DNA sequences. Globin Gene Server informs about human hemoglobin mutations. It offers a list of experimental data and several types of software allowing comparison to find regions that are likely to play significant roles.
Offers a manually curated dataset of promiscuous enzymes and related information. ProtMiscuity centralizes experimentally characterized examples of this phenomenon. It contains more than 80 described chemical reactions in proteins coming from 40 different organisms. This tool allows users to investigate putative catalytic activities and their underlying mechanisms. It is useful for retrieving complete information to develop and test computational tools for the study and prediction of promiscuous behavior.
Functional annotation of protein aims to extend the knowledgebase of existing, novel or relatively less studied proteins by using a number of computational techniques. Existing knowledgebase of well-studied proteins are used for prediction. Protannotator integrates a suite of bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology, and biochemical pathways.
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.