Chemistry: 6. Biochemistry

Searchable dictionary of 3000 terms from biochemistry and genetics.

Terms in genetics and biochemistry are defined, with audio pronunciations, illustrations, and animations. From the National Human Genome Project at NIH.

PubChem provides information on the biological activities of small molecules.

BLAST finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

A comprehensive database of enzymes with original literature references, organism-related information, etc.

Database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data)

KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from genomic and molecular-level information.

A freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

A unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 6707 drug entries including 1436 FDA-approved small molecule drugs, 134 FDA-approved biotech (protein/peptide) drugs, 83 nutraceuticals and 5086 experimental drugs.

The first free, open-access database of antibacterial compounds, including discontinued agents, drugs under pre-clinical development and those in clinical trials. This database includes over 1000 compounds.

Chemotext mines the published literature in PubMed using MeSH subject terms to enable text-based drug-target-disease relationships in order to identify novel drug repurposing candidates and discovery targets.

The LIPID MAPS consortium provides a range of tools and resources to facilitate lipid research.

The official database of Japanese Conference on the Biochemistry of Lipids (JCBL)

BLAST finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function, and visualize, download, and analyze the results.

Tools for searching and analyzing protein sequences based on mass spectroscopy.

BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.

Enter a PDB (Protein Data Bank) format file of the protein model, and get back a list of predicted 13C chemical shifts for each amino acid residue in the sequence.

Eidogen-Sertanty's database of kinase structure-activity and chemical synthesis data.

Public access service for structure-based ligand discovery. Aims to answer the question: What small molecules should I purchase and test for activity against my biological target for which I have a structure?

STITCH is a resource to explore known and predicted interactions of chemicals and proteins.

Facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS).

METLIN is a metabolite database for metabolomics containing over 42,000 structures, it also represents a data management system designed to assist in a broad array of metabolite research and metabolite identification by providing public access to its repository of current and comprehensive MS/MS metabolite data.

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1790 pathways from more than 2216 different organisms, and is curated from the scientific experimental literature.

A freely available electronic database containing detailed information about small molecule metabolites found in the human body.