Links

Structural Domain Databases

• 3Dee: contains structural domain definitions for all protein chains in the Protein Databank (PDB).
• CATH: hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class©, Architecture(A), Topology(T) and Homologous superfamily (H).
• DALI: A network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank.
• SCOP: Provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.
• Pawson Lab – Protein interaction domains: Focus is on studying the mechanisms that underlie intracellular signal transduction. Modular protein domains that mediate protein-protein interactions are critical elements of this process.
• Nash Lab – Protein interaction domains in Signal Transduction: Research lab that focuses on protein interaction domains and other areas.
• Definition and assignment of structural domains in proteins: a resource centered around definition and assignment of structural domains in proteins.
• EMBL-EBI: Tools from Dali-server:
  1. MaxSprout: A fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. Can be downloaded from site.
  2. FSSP: a database of structural alignments of proteins in the Protein Data Bank (PDB).
  3. DSSP: Search to standardize secondary structure assignment.
  4. DaliLite Pairwise comparison: a program for pairwise structure comparison and for database searching. It does not create or update the database searched against, which is available from EBI. Can be downloaded from site.
  5. Database Search Form: Submit the 3D coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank.

Sequence Domain Databases

• InterPro: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. Has a scan for protein sequences, but each scan must be done individually.
• Pfam: Find domains on a PDB structure; analyze your protein sequence for Pfam matches. Protein families are represented by HMMs and MSAs and you can see groups of families.
• PROSITE: Describes protein domains, functional cites, and families. Also has associated profiles and patterns to identify them. Features a quick scan (Run a sequence against Prosite patterns and profiles), and has a new image creater for custom domain figures. (1494 documentation entries, 1319 patterns, 746 profiles and 764 ProRule)
• ProDom: Related software: Generate and visualize sequence families using your own data. Database of automatic compilation of homologous domains.
• SMART : Allows for identification and annotation of genetically mobile domains. The focus of SMART is to search for evolutionarily conserved protein domains rather than small sites of post-translational modification.It is also composed of diff. components and one needs a license agreement (free for academic uses) to use HMMs
• NCBI Conserved Domain Database: A collection of multiple sequence alignments for ancient domains and full-length proteins.

Protein Searches

• UniProt: Consist of protein sequence entries.
• Prints: Compendium of Protein fingerprints.
• TIGRFAMs: Collection of Protein families.
• PANTHER HMMs: Define protein families and subfamilies modeled on the divergence of function.
• PIRSF: Classification system based on evolutionary relationship of whole protein.
• Superfamily: Has a library of HMMs that represent all proteins of known structure, based on SCOP.
• Gene3D: Extended predictions of CATH protein structures.
• MSD: Collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).
• MODBASE: Models are generated by fully automated homology- modeling pipeline MODPIPE.
• SWISS-MODEL: Fully automated protein structure homology-modeling server.

SNP Databases

• ALFRED: The ALlele FREquency Database
• CGAP SNP index: An index of UniGene assemblies and our most current build of predicted SNP locations, searchable by gene, description, or nucleotide sequence.
• CHIP Bioinformatics Portal
• dbSNP: Database of Single Nucleotide Polymorphisms
• dbQSNP: A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.
• FESD: Functional element SNP database
• Forensic SNP Information: Provides general information on single nucleotide polymorphism (SNP) markers that may be of interest in human identification applications.
• Gene Viewer: displays SNPs in mRNA sequences
• GeneSNPs
• Glovar: Glovar shows sequence variation in a genomic context (EnsEMBL/Sanger)
• HGVBASE Human Genic Bi Allelic SEquences
• International HapMap Project: The site for the International HapMap Project includes project information and genotype data.
• Human SNP Database: Search for SNPs by name or by Source STS.
• IIPGA: The Innate Immunity PGA project has data for ~83 innate immunity genes.
• NCBI
• Japanese SNP Database: A database of Japanese Single Nucleotide Polymorphisms.
• PhenCode: variants from locus-specific databases displayed in the UCSC genome browser.
• SNAP: a SNP annotation platform.
• SNP@WEB: a web-based catalog of databases and tools for SNP studies.
• SNP500Cancer Database
• SNPpipe: SNP selection pipeline.
• SNPper: Retrieve known SNPs by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions.
• Tagger: tool for the selection and evaluation of tag SNPs from genotype data
• The SNP Consortium Home Page
• TopoSNP database: visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and display of geometric and relative entropy calculations
• TSC: The SNP Consortium – single nucleotide polymorphisms for biomedical research.
• UCSC: The UCSC Genome Browser Annotation Database.
• UW-FHCRC Variation Discovery Resource: Washington School of Research