'The BindingDB is a public, web-accessible 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 (ITC) and enzyme inhibition (Enz. Inhib.) methods; other techniques will be included in the future. ... [Information of the supplier]
ChemMine is a compound mining database that facilitates drug and agrochemical discovery and chemical genomics screens. Its web service is divided into three major functional components: (1) Compound Database, comprising Annotation Search and Structure Search; (2) Cheminformatics Workbench; and (3) Screening Database. A detailed tutorial for using ChemMine's online services is available on the ReadMe page. ... [Information of the supplier, modified]
The Structural Genomics Consortium (SGC) is a not-for-profit organization that aims to determine the three dimensional structures of proteins of medical relevance, and place them in the public domain without restriction. The SGC operates out of the Universities of Oxford and Toronto and Karolinska Institutet, Stockholm. The SGC works on structures of proteins from its Target List of ~2,000 proteins, which comprises human proteins associated with diseases such as cancer, diabetes, inflammation, and genetic diseases, as well as proteins from human parasites such as those that cause malaria. Research at the SGC is divided into three areas: structural genomics of soluble proteins, structural genomics of integral membrane proteins, and structural chemistry of soluble proteins. ... [Information of the supplier]
The Biological Biochemical Image Database is a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics. [Information of the supplier]
Cell Circuits is an open-access database of molecular network models that: (a) Bridges the gap between databases of individual pair-wise molecular interactions and databases of validated pathways. (b) Contains functional network hypothesis produced by algorithms that screen molecular interaction networks based on their correspondence with expression or phenotypic data, their internal structure, or their conservation across species. (c) Is searchable using protein/gene names and Gene Ontology terms. Models are available either as images or in machine-readable formats. (d) Serves as a clearinghouse in which theorists may distribute or revise models in need of validation and experimentalists may search for models or specific hypotheses relevant to their interests. ... [Information of the supplier, modified]
EBIMed is a web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. You can type term queries in the text box provided following the syntax conventions that can be found here. Your terms will be looked up throughout Medline and several abstracts will thus be retrieved and analysed. In the simple interface the higher limit is 500 to make the process quick. You can set a higher limit through the Advanced Search interface. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading. ... [Information of the supplier, modified]
Today, vast amounts of protein-small molecule binding sites can be found in the Protein Data Bank (PDB). Exhaustive comparison of them is computationally demanding, but useful in the prediction of protein functions and drug discovery. We proposed a tremendously fast algorithm called "SketchSort" that enables the enumeration of similar pairs in a huge number of protein-ligand binding sites. We conducted all-pair similarity searches for 3.4 million known and potential binding sites using the proposed method and discovered over 24 million similar pairs of binding sites. We present the results as a relational database Pocket Similarity Search using Multiple-Sketches (PoSSuM), which includes all the discovered pairs with annotations of various types (e.g., CATH, SCOP, EC number, Gene ontology). PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures. Basically, the users can search similar binding pockets using two search modes: i) "Search K" is useful for finding similar binding sites for a known ligand-binding site. Post a known ligand-binding site (a pair of "PDB ID" and "HET code") in the PDB, and PoSSuM will search similar sites for the query site; ii) "Search P" is useful for predicting ligands that potentially bind to a structure of interest. Post a known protein structure (PDB ID) in the PDB, and PoSSuM will search similar known-ligand binding sites for the query structure. ... [Information of the supplier]
Rhea is a reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. We have populated the database with the reactions found in the EC list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalysed reactions, other biochemical reactions (including those that are often termed "spontaneous") also are included. Rhea is a manually annotated resource and it provides: a)Stable reaction identifiers for each of its reactions. These identifiers are independent of EC numbers but are linked to EC numbers via cross-references; b)Directionality information if the physiological direction of the reaction is known; c)The possibility to link several reactions together to form complex reactions. This feature can also be used to split reactions into partial reactions; d)Extensive cross-references to other resources including enzyme-catalysed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; e)Chemical substructure and similarity searches on compounds in Rhea, thereby allowing reactions to be found where similar compounds are involved. The database is extensively cross-referenced. Reactions are currently linked to the EC list, KEGG and MetaCyc, and the reactions will be used in the IntEnz database and in all relevant UniProtKB entries. Furthermore, the reactions will also be used in the UniPathway database to generate pathways and metabolic networks. ... [Information of the supplier]
