Databases

This section contains databases of biologically relevant enzymes, molecules and drugs.

Found 37 links

Displaying 15 links

BioDrugScreenDatabase Content

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BioDrugScreen is a resource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on 1589 human targets resulting in >3 million receptor-ligand complexes. The targets in BioDrugScreen originated from Human Cancer Protein Interaction Network, which we have updated, as well as the Human Druggable Proteome, which we have created for the purpose of this effort. This makes the BioDrugScreen resource highly valuable in drug discovery.

CAMPDatabase Content

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Collection of Anti-Microbial Peptides (CAMP) is a free online database that is manually curated and currently holds 3782 antimicrobial sequences. These sequences are divided into experimentally validated (patents and non-patents: 2766) and predicted (1016) datasets based on their reference literature. Information like source organism, activity (MIC values), reference literature, target and non-target organisms of AMPs are captured in the database. Prediction and sequence analysis tools, including BLAST, are integrated in the database.

CancerResourceDatabase Content

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CancerResource, a database that integrates cancer-relevant relationships of compounds and targets from (i) literature mining and (ii) external resources complemented with (iii) essential experimental and supporting information on genes and cellular effects. CancerResource addresses the spectrum of research on compound-target interactions in natural sciences as well as in individualized medicine.

This content is being maintained by robertpreissner.

ChEBIDatabase Content

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Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities.

links directory index: 97
TitlePublication YearGoogle Scholar Citation Count
Chemical Entities of Biological Interest: an update201097

ChemProtDatabase Content

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ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). The PPI network layer allows for studying disease and tissue specificity through each protein complex. ChemProt can assist in the in silico evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events.

This content is being maintained by otab.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
ChemProt: a disease chemical biology database201110

DAMPDDatabase Content

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Dragon AntiMicrobial Peptide Database: manually curated database of known and putative antimicrobial peptides.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
DAMPD: a manually curated antimicrobial peptide database20121

DOMMINODatabase Content

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Database of Macromolecular interactions. Includes interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
DOMMINO: a database of macromolecular interactions20121

Drug2GeneDatabase Content

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Drug2Gene is a free database unifying popular public resources to provide structured and organized information for identified and reported relations between genes/proteins and drugs/compounds. You can flag, comment and update relations, import new drug-gene relations valuable for a specific project. Gene orthology and similarity info is matched to certain entries assisting the prediction of new unreported drug-gene associations. Available links to the original source of the reported relation.

This content is being maintained by Ivanka_Karageorgieva_metalife.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

DrugBank 3.0Database Content

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DrugBank is a richly annotated database of drug and drug target information. It contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pharmaceutical properties of both small molecule and large molecule (biotech) drugs. It also contains comprehensive information on the target diseases, proteins, genes and organisms on which these drugs act. New data field additions include illustrated drug-action pathways, drug transporter data, drug metabolite data, pharmacogenomic data, adverse drug response data, ADMET data, pharmacokinetic data, computed property data and chemical classification data. DrugBank 3.0 also offers expanded database links, improved search tools for drug-drug and food-drug interaction, new resources for querying and viewing drug pathways and hundreds of new drug entries with detailed patent, pricing and manufacturer data.

EDULISSDatabase Content

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EDULISS (EDinburgh University Ligand Selection System) database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for unique compound recognition is demonstrated by making use of small subgroups of the descriptors.

EMDataBank.orgDatabase Content

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EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
EMDataBank.org: unified data resource for CryoEM201115

FragmentStoreDatabase Content

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FragmentStore, a resource for the comparison of fragments found in metabolites, drugs or toxic compounds. Starting from 13,000 metabolites, 16,000 drugs and 2200 toxic compounds we generated 35,000 different building blocks (fragments), which are not only relevant to their biosynthesis and degradation but also provide important information regarding side-effects and toxicity. The FragmentStore provides a variety of search options such as 2D structure, molecular weight, rotatable bonds, etc. Various analysis tools have been implemented including the calculation of amino acid preferences of fragments' binding sites, classification of fragments based on the enzyme classification class of the enzyme(s) they bind to and small molecule library generation via a fragment-assembler tool.

This content is being maintained by robertpreissner.

FunTreeDatabase Content

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FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH .

GlycomeDBDatabase Content

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GlycomeDB integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank. The database is a unified resource for carbohydrate structures. GlycomeDB retains the links to the original databases and is updated at weekly intervals with the newest structures available from the source databases.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
GlycomeDB--a unified database for carbohydrate structures20112

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