Bioinformatics Resources and Tools

The Protein Information Resource (PIR) is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies.
It includes PRO, iProClass, iProLink, Reference Proteomes (RPs), iProXpress and iPTMnet.

The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).
UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR). It integrates Swiss-Prot and TrEMBL.

InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. InterPro combines signatures from multiple, diverse databases into a single searchable resource, reducing redundancy and helping users interpret their sequence analysis results.

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) covering many common protein domains.

PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family a new sequence belongs.

SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.

Geno3D is an automatic web server for protein molecular modelling of three-dimensional structure.

The Protein Databank -- Protein 3D structure database, is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins, and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans.

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).

The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.

STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases.

The Bayesian algorithm expicitly models the amino acid composition of interacting kinase / regulator pairs to predict interaction specificity of orphan kinases and regulators across all sequenced bacterial genomes.