The University of Texas

Biochemical Information

recommended resource : Recommended

Binding Database
The BindingDB is a public database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds.The database currently contains data generated by isothermal titration calorimetry, enzyme inhibition, and receptor-ligand binding methods.

BioCyc Database Collection
"BioCyc is a collection of 3530 Pathway/Genome Databases (PGDBs), with tools for understanding their data. "

Biological Macromolecule Crystallization Database (BMCD)
The Biological Macromolecule Crystallization Database (BMCD) contains crystal data and the crystallization conditions, which have been compiled from literature. The current version of the BMCD includes 5247 crystal entries from macromolecules for which diffraction quality crystals have been obtained. These include proteins, protein:protein complexes, nucleic acid, nucleic acid:nucleic acid complexes, protein:nucleic acid complexes, and viruses.

BRENDA: Comprehensive Enzyme Information System recommended resource
Free database containing information on over 3500 enzymes: nomenclature, EC and registry numbers, reaction and specificity, inhibitors, structure, isolation, literature references, etc. (Cologne University Bioinformatics Center)

Carcinogenic Potency Database
Provides "results of 6540 chronic, long-term animal cancer tests on 1547 chemicals. The CPDB provides easy access to the bioassay literature, with qualitative and quantitative analyses of both positive and negative experiments that have been published over the past 50 years in the general literature through 2001 and by the National Cancer Institute/National Toxicology Program through 2004." (UC Berkeley)

ChEBI: Chemical Entities of Biological Interest
Dictionary of small molecular entities that are natural or synthetic products used to intervene in the processes of living organisms. Data drawn from public files such as IntEnz and KEGG LIGAND, etc.

"ChemBank is intended to guide chemists synthesizing novel compounds or libraries, to assist biologists searching for small molecules that perturb specific biological pathways, and to catalyze the process by which drug hunters discover new and effective medicines. (Broad Institute)

"ChEMBL is a 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)." (European Bioinformatics Institute)

ChemDB is a suite of chemical datasets and learning tools created by UC Irvine. Includes a chemical search feature for about 4 million compounds from vendor catalogs.

"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 7685 drug entries including 1549 FDA-approved small molecule drugs, 155 FDA-approved biotech (protein/peptide) drugs, 89 nutraceuticals and over 6000 experimental drugs. Additionally, 4282 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data."

ENZYME recommended resource
"ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided." (ExPASy)

Enzyme Explorer
Search by name, application, specificity or EC number. The Enzyme Explorer also features detailed sites on metabolic pathways, protein kinases, protease specificity and inhibition, and glycoprotein analysis as well as new cell signaling, analytical and diagnostic enzymes and reagents. (Sigma-Aldrich)

Enzyme Nomenclature
Subtitle: "Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse." Browse and search for enzyme names using EC numbers.

"ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc."

GenBank recommended resource
"GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI."

Genome Bioinformatics
Contains the reference sequence and working draft assemblies for a large collection of genomes. (UC Santa Cruz)

"GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences." (Kyoto University)

"The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors." (NIH)

Human Metabolome Database
"The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data."

"LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major — and many minor — lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation." (NIH)

Molinspiration Cheminformatics
Free web site with Java-based (JME) interface for searching substructure, similarity and pharmacophore similarity on a collection of molecules. Also offers a chemical property calculation function for determining estimated logP (octanol-water partition coefficient), PSA, etc.

National Center for Biotechnology Information (NCBI) recommended resource
Parent site of the major NLM databases, including PubMed, GenBank, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, PubChem, and others. (NIH)

Nucleic Acid Database recommended resource
"The NDB contains information about experimentally-determined nucleic acids and complex assemblies. Use the NDB to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and learn about nucleic acids." (Rutgers University)

OSIRIS Property Explorer
Calculates on-the-fly drug-relevant properties (cLogP, solubility, MW) from a valid structure. Prediction results are valued and color coded. (Actelion)

Protein Data Bank recommended resource
The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.

A wiki site that aims to collect, organize and disseminate structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules.

NIH cheminformatics database on biological activities of small molecules primarily of interest to pharmaceutical and chemical genomics researchers. PubChem includes substance information, compound structures, and BioActivity data in three primary databases. The Substance/Compound database, where possible, provides links to BioAssay description, literature, references, and assay data points. PubChem is integrated with Entrez, NCBI's primary search engine, and also provides compound neighboring, sub/superstructure, similarity structure, BioActivity data, and other searching features. Links from PubChem's chemical structure records to other Entrez databases provide information on biological properties. These include links to PubMed scientific literature and NCBI's protein 3D structure resource. Links to depositor web sites provide further information. (NIH does not take responsibility for the accuracy of the deposited data, and errors can be rapidly propagated across multiple online databases.)

SCOPe - Structural Classification of Proteins
"Structural Classification of Proteins — extended (SCOPe) is a database of protein structural relationships that extends the SCOP database. SCOP is a (mostly) manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships." (UC Berkeley)

STITCH: Chemical-Protein Interactions
"STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. STITCH contains interactions for between 300,000 small molecules and 2.6 million proteins from 1133 organisms."

UniProt (Universal Protein Resource) is a central repository of protein sequence and function data, merging the information contained in Swiss-Prot, TrEMBL, and PIR.

Database of "commercially-available compounds for virtual screening. ZINC contains over 35 million purchase-able compounds in ready-to-dock, 3D formats." (UC San Francisco)


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