Proteins
Main Page >> Protein Information
Entrez
Proteins - search protein sequence records (from GenPept + RefSeq
+ Swiss-Prot + PIR + RPF + PDB) by accession number, author name, organism,
gene/protein name, and a variety of other text terms
RefSeq -
NCBI database of Reference Sequences. Curated, non-redundant set including
genomic DNA contigs, mRNAs and proteins for known genes, mRNAs and proteins
for gene models, and entire chromosomes.
FTP GenPept -
download the "genpept.fsa.Z" file, which contains FASTA formatted
amino acid translations extracted from GenBank/EMBL/DDBJ records that
are annotated with one or more CDS features
Conserved
Domain Database (CDD) - a collection of sequence alignments and
profiles representing protein domains conserved in molecular evolution.
It includes domains from Smart and Pfam,
as well as domains contributed by NCBI researchers.
PROW -
Protein Resources on the Web - short authoritative guides on the approximately
200 human CD cell-surface molecules. Peer-reviewed; provides approximately
20 standardized categories of information (biochemical function, ligands,
etc.) for each CD antigen.
Protein
Sequence Analysis - various tools are available for analyzing
protein sequences
Protein Data Bank -
t he single worldwide repository for the processing and distribution
of 3-D biological macromolecular structure data.
CluSTr Offers
an automatic classification of UniProt/Swiss-Prot + UniProt/TrEMBL.
CSA ***
CSA - The Catalytic Site Atlas is a resource of catalytic sites and residues
identified in enzymes using structural data.
GO ***
The EBI's Gene Ontology consortium pages. GO is an international consortium
of scientists with the editorial office based at the EBI.
GOA ***
Provides assignments of gene products to the Gene Ontology (GO) resource.
HPI Human
Proteomics Initiative (HPI) is an initiative, by SIB and
the EBI, to annotate all known human sequences according to the quality
standards of UniProt/Swiss-Prot.
IntAct ***
IntAct is a protein interaction database and analysis system. It provides
a query interface and modules to analyse interaction data.
IntEnz ***
The Integrated relational Enzyme database (IntEnz) will contain enzyme
data approved by the Nomenclature Committee. The goal is to create a
single relational enzyme database.
InterPro ***
The InterPro database is an integrated documentation resource for protein
families, domains and functional sites.
IPI International
Protein Index a non-redundant human proteome set constructed from UniProt/Swiss-Prot,
UniProt/TrEMBL, Ensembl and RefSeq.
PANDIT ***
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees.
PANDIT is a collection of multiple sequence alignments and phylogenetic
trees covering many common protein domains.
Proteome
Analysis
Statistical and comparative analysis of the predicted proteomes of fully
sequenced organisms.
UniProt/Knowledgebase ***
A centralised resource for protein sequences and is the central hub for
the collection of functional information on proteins, with accurate,
consistent, and rich annotation, the amino acid sequence, protein name
or description, taxonomic data and citation information.
UniProt/UniParc ***
Features clustering of similar sequences to yield a representative subset
of sequences. This produces very fast search times.
UniProt/UniRef ***
A non-redundant archive of protein sequences extracted from public databases
and contains only protein sequences.
UniProt/Swiss-Prot An
annotated protein sequence database. Part of the UniProt Knowledgebase.
UniProt/TrEMBL A
computer generated protein database enriched with automated classification
and annotation. Part of the UniProt Knowledgebase.
ExPASY Molecular Biology Server -
is dedicated to the analysis of protein sequences and structures as well
as 2-D PAGE
Molecular
Model Database –NCBI molecular structure database
Conserved
Domain Database
Membrane
Protein resources
Vector
Alignment Search Tool (VAST) is a service that allows searching
for structural neighbors starting with a set of 3D-coordinates specified
by the user.
3D
Structure Viewer Freeware (Cn3D) Cn3D is a helper application for
your web browser that allows you to view 3-dimensional structures from
NCBI's Entrez retrieval
service.
Database of Quantitative
Cellular Signaling (DOQCS) - is a repository of models of signaling
pathways. It includes reaction schemes, concentrations, rate constants,
as well as annotations on the models. The database provides a range
of search, navigation, and comparison functions.
Cytoscape -
A bioinformatics software platform for visualizing molecular
interaction networks and integrating these interactions with
gene expression profiles and other state data
Kyoto Encyclopedia
of genes and genomes (pathways)
Additional
on-line resources – other databases for protein interactions
and protein structure |
