Database of Interacting Proteins (DIP) | UCLA
Data on experimentally determined interactions between proteins. DIP combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database was manually curated by subject experts and also automatically using computational approaches.
IntAct | EMBL-EBI
Database: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
PRIDE Database | EMBL-EBI
is a centralized, standards compliant, public data repository for proteomics data. It has been developed to provide the proteomics community with a public repository for protein and peptide identifications together with the evidence supporting these identifications.
ExPASy Proteomics Server | Swiss Institute of Bioinformatics (SIB)
allows users to browse through a number of databases, such as Swiss-Prot, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE, ENZYME, as well as other cross-referenced databases.
GFS Web | Giddings Lab at UNC
Web-based tool that maps peptide mass fingerprint data directly to their genomic origin, allowing for genome-based, annotation-independent protein identification.
Proteomic Standards Initiative | Human Proteome Organisation's (HUPO)
The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification.
Human Protein Reference Database (HPRD) | PadyLab and Institute of Bioinformatics
HPRD contains annotations to human proteins based on experimental evidence.
InterProScan | EMBL-EBI
InterPro is a collaborative project aimed to provide a unique, non- redundant characterization of a given protein family, domain or functional site. InterProScan is a extensible search interface for search InterPro.
Mascot | Matrix Science
Mascot is a search engine which uses mass spectrometry data to identify proteins from primary sequence databases. There are three different search methods for searching Mascot:
- Peptide Mass Fingerprint in which the only experimental data are peptide mass values
- Sequence Query in which peptide mass data are combined with amino acid sequence and composition information. A super-set of a sequence tag query
- MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides
MINT | University of Rome Tor Vergata
The Molecular INTeraction database contains information about molecular interactions of proteins by extracting experimental details from work published in peer-reviewed journals. Genetic or computationally inferred interactions are not included in the database.
Protein Data Bank | Research Collaboratory for Structural Bioinformatics (RCSB)
Tool that provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
ProtScal | EXPASY
Allows users to compute and represent (in the form of a two-dimensional plot) the profile produced by any amino acid scale on a selected protein.
Protein Structure Prediction Server (PSIPRED) | Department of Computer Science at University College London (UCL)
Web-based tool from that allows a user to submit a protein sequence, perform a prediction and receive the results of the prediction via e-mail.
Protein Prospector | UCSF Mass Spectrometry Facility
Proteomics tools for mining sequence database using data from Mass Spectrometry experiments.
Structural Classification of Proteins (SCOP) | Berkeley
Manually curated database that seeks to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.