Molecular Biology Web Resources

Protein Sequences, Structures & Family
Taxonomy
Biological Culture and Stock Collection Databases

Gene & Gene Expression

Gene
- Entrez Gene (NCBI) is a database for gene-specific information. (Tutorial)
Gene Expression
- GEO: Gene Expression Omnibus (NCBI) is a public repository for a variety of high-throughput experimental data including data from microarray-based experiments measuring mRNA, genomic DNA, and protein abundance.
- ArrayExpress (EBI) stores gene-indexed expression profiles from a curated subset of experiments in the repository.
- SAGE Genie (NCI) provides visual displays of human and mouse gene expression, based on a an analytical process that reliably matches SAGE tags to known genes.

Nucleotide Sequence Databases

Nucleotide Sequence Databases
- Entrez Nucleotide (NBCI) is a collection of sequences from several sources, including GenBank, RefSeq, and PDB.
- RefSeq (NCBI) collects a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
- EMBL-Bank (EMBL-EBI) constitutes Europe's primary nucleotide sequence resource.
- DDBJ DNA database of Japan
Nucleotide Sequence Tools
- BLAST (NCBI) - sequence similarity searching | Tutorial
- Nucleotide Sequence Tools (NCBI)

Protein Sequences, Structures, & Family

Protein Sequence Databases
- Entrez Protein database (NCBI) is derived from several protein databases (Swiss-Prot, PIR, PDB) and translations of the GenBank nucleotide sequence records.
- Swiss-Prot (SIB) is a manually curated and extensively annotated protein sequence database with a minimal level of redundancy.
- PIR: Protein Information Resource (Georgetown) contains classified and functionally annotated protein sequences. The database is nonredundant and annotated by experts.
- UniProt: Universal Protein Resource is a collaboration between the EBI, SIB and PIR. It provides access to extensive and expertly curated protein information, including function, classification and cross-references.
Protein Sequence Analysis and Proteomics
- BIOBASE Proteome Knowledge Library
- BLAST (NCBI) - sequence similarity searching | Tutorial
- FASTA (EMBL - EBI) - protein sequence alignment method
- Protein Sequence Analysis Tools (NCBI)
- Astral Compendium (UC Berkeley) - sequence and structure analysis
Protein Structure Databases
- PDB: Protein Data Bank is the priimary database archive of experimentally determined three-dimensional structures of proteins and protein complexes. | Tutorial
- MMDB: Molecular Modeling Database (NCBI) contains 3D protein structures obtained primarily from X-ray crystallography and NMR spectroscopy. The data is a subset of the PDB database.
- EBI Structural Databases contains a number of protein structure related databases
Protein Family & Domain Databases
- CDD: Conserved Domain Database (NCBI) is a collection of multiple sequence alignments for ancient domains and full-length proteins.
- InterPro (EBI) is a database of protein families, domains, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.
- Prosite (SIB) contains database of protein families and domains
- Berkeley Phylogenomics Group Phylogenomic classification of proteins into families and subfamilies
- Database of Macromolecular Movements (Yale U)
Structure Graphic Viewer
- Cn3D (NCBI) - 3D structure viewer at NCBI
- NDB (Rutgers) 3D Nucleic Acide Database Structure
- Rasmol (UMass) - Protein Explorer at UMass Amherst
- Structural Classification of Proteins (Cambridge)

Taxonomy

Entrez Taxonomy Browser (NCBI) search or browse taxonomic information.
Integrated Taxonomic Information System contains taxonomic information for plants, animals, fungi, and microbes.
Tree of Life Web Project is a browseable tree of taxonomic classification, with information for each species.

Biological Culture and Stock Collection Databases

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