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]
Dieses Portal soll einen groben Überblick über die Inhalte und Nutzung von wichtigen online-Datenbanken mit biochemischen Inhalten verschaffen. Am wichtigsten sind hier wohl die Datenbanken mit Informationen über Proteine und Gene, es werden jedoch auch Datenbanken für organische Verbindungen oder verschiedene Organismen aufgeführt. BioKemika ist die zentrale Informationsplattform für Biochemie-Studenten der Goethe Universität in Frankfurt am Main. Jeder kann mit seinem Wissen beitragen. Seit April 2009 sind so 55 Artikel entstanden, die in folgenden Portalen organisiert sind: Lehre, Forschung, Bioinformatik, Studium, Mitmachen, Projektinfo, Seminare. ... [Information des Anbieters, verändert]
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]
The purpose of the BioSamples database is to provide unified storage and access to information about biological samples. These samples may have investigation information stored in other databases (e.g. sequencing, structure, expression). Physical samples may also be available for further study from suppliers. The definition of a sample is flexible. Most samples are straightforward, such as tissue from an individual organism. However, a sample can also be an environmental sample (e.g. for meta-genomic analysis), a hybrid between two species, infected tissue, etc. Within the BioSamples Database, collections of samples are managed as "submission". Each submission is one SampleTab format file emailed to biosamples@ebi.ac.uk. Some highly-curated and highly-referenced submissions may become "reference samples", for example the ENCODE cell lines. These are samples that are of particular interest and have datasets from multiple technologies associated with them. ... [Information of the supplier]
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]
