LibGuides: Biochemistry and Molecular Biology: Databanks

Enzymes

Image: Decarboxylation reaction of alpha-keto acids. NEUROtiker. Public domain. Wikimedia Commons.

* Highly recommended websites.

BRENDA * Data on over 5,000 enzymes: nomenclature, structure, function, isolation, preparation, etc.
Enzyme Nomenclature* Repository of information relative to the nomenclature of enzymes.
Enzyme Structures This database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB).
MEROPS: the Peptidase Database An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them
Restriction Enzyme Database A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included.

Genes and Genomes

Image: Human genome. Webridge. CC BY 2.0. Wikimedia Commons.

* Highly recommended websites.

NCBI Gene * Gene maintains information about genes from genomes of interest to the RefSeq group.
Ensembl The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
USCS Genome Bioinformatics This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects.
NCBI Genome This resource organizes information on genomes including maps, chromosomes, assemblies, and annotations.
NCBI Genomes and Maps Databases Collection of genome database links.
TargetScanHuman

Macromolecules

Image: Syndiotactic Polypropene Model. Ilmari Karonen. Public Domain. Wikimedia Commons.

* Highly recommended websites.

RCSB Protein Data Bank * An Information Portal to Biological Macromolecular Structures.
BMRB BioMagResBank Provides data from NMR spectroscopic investigations of biological macromolecules on proteins, peptides and nucleic acids.
Structure Three dimensional structures of macromolecules. May can be used to examine sequence-structure-function relationships, interactions, active sites, and more.

Nucleic Acids

Image: GAAA Tetraloop and Receptor. Qinhua Zhou. CC-BY-3.0. Wikimedia Commons.

* Highly recommended websites.

BLAST*
miRBase Each entry represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).
Nucleotide Database The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

Portals

Image: 3 D Model of Biotin molecule. Michael Ströck. GNU. Wikimedia Commons.

Biological Information Resources Centralized biological sequence databases: DNA Analysis Tools, Protein Analysis Tools, Database Search Tools, Sequence Analysis Sites, Protein and Protein Families, Genomes, Molecular Biology and Genetics Links.
NCBI The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
Nucleic Acids Research Databases Collection of nucleic acid research databases.

Proteins

Image: Lipoamide. By Doxepine. Public Domain. Wikimedia Commons.

* Highly recommended websites.

RCSB Protein Data Bank * Contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
ExPASy Proteomics Server * Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.
BMRB: Biological Magnetic Resonance Data Bank A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
COGs - Clusters of Orthologous Groups (of proteins) Phylogenetic classification of proteins encoded in complete genomes.
InterPro InterPro is an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures.
NCBI Protein 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. Protein sequences are the fundamental determinants of biological structure and function.
PRINTS PRINTS is a compendium of protein fingerprints.
PROSITE PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Robetta: Full Chain Protein Structure Prediction Server Robetta provides both ab initio and comparative models of protein domains.
UniProt Protein sequence and functional information.

Small Molecules

Image: Structure schematic of human SUMO1 protein. By Jakob Suckale. Public Domain. Wikimedia Commons.

* Highly recommended websites.

CHEMBL * A manually curated chemical database of bioactive molecules with drug-like properties.
SDBS Spectral database for organic compounds.
NIST Chemistry WebBook Spectral database.
PubChem* NLM's single source for chemical information.
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A database of chemical molecules and their activities against biological assays.