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Found 18 result(s)

Kyoto Encyclopedia of Genes and Genomes

KEGG

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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 molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies

Reactome

a curated pathway database

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Reactome is a manually curated, peer-reviewed pathway database, annotated by expert biologists and cross-referenced to bioinformatics databases. Its aim is to share information in the visual representations of biological pathways in a computationally accessible format. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.

PSnpBind

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PSnpBind is a large database of protein–ligand complexes covering a wide range of binding pocket mutations and small molecules’ landscape. This database can be used as a source of data for different types of studies, for example, developing machine learning algorithms to predict protein–ligand affinity or mutation's effect on it which requires an extensive amount of data with a wide coverage of mutation types and small molecules. Also, studies of protein-ligand interactions and conformer orientation changes across different mutated versions of a protein can be established using data from PSnpBind.

UniSave

UniProtKB Sequence/Annotation Version Archive

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The UniProtKB Sequence/Annotation Version Archive (UniSave) has the mission of providing freely to the scientific community a repository containing every version of every Swiss-Prot/TrEMBL entry in the UniProt Knowledge Base (UniProtKB). This is achieved by archiving, every release, the entry versions within the current release. The primary usage of this service is to provide open access to all entry versions of all entries. In addition to viewing their content, one can also filter, download and compare versions.

NASC

The European Arabidopsis Stock Centre

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The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to Europe researchers.

ChEMBL

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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). The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs We attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.

Mechanism and Catalytic Site Atlas

CSA (formerly)

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M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. The M-CSA (Mechanism and Catalytic Site Atlas) represents a unified resource that combines the data in both MACiE and the CSA

SureChEMBL

Open Patent Data

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SureChemOpen is a free resource for researchers who want to search, view and link to patent chemistry. For end-users with professional search and analysis needs, we offer the fully-featured SureChemPro. For enterprise users, SureChemDirect provides all our patent chemistry via an API or a data feed. The SureChem family of products is built upon the Claims® Global Patent Database, a comprehensive international patent collection provided by IFI Claims®. This state of the art database is normalized and curated to provide unprecedented consistency and quality.

STRING

Known and Predicted Protein-Protein Interactions

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STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: - Genomic Context - High-throughput Experiments - (Conserved) Coexpression - Previous Knowledge STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.

DrugBank

Open Data Drug & Drug Target Database

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The DrugBank database is 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 latest release of DrugBank (version 5.1.1, released 2018-07-03) contains 11,881 drug entries including 2,526 approved small molecule drugs, 1,184 approved biotech (protein/peptide) drugs, 129 nutraceuticals and over 5,751 experimental drugs. Additionally, 5,132 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.

MetaCyc

Metabolic Pathway Database

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MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. MetaCyc applications include: Online encyclopedia of metabolism, Prediction of metabolic pathways in sequenced genomes, Support metabolic engineering via enzyme database, Metabolite database aids. metabolomics research.

SwissLipids

Swiss+Lipids

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SwissLipids is an expert curated resource that provides a framework for the integration of lipid and lipidomic data with biological knowledge and models.

HumanCyc

Encyclopedia of Human Genes and Metabolism

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HumanCyc provides an encyclopedic reference on human metabolic pathways. It provides a zoomable human metabolic map diagram, and it has been used to generate a steady-state quantitative model of human metabolism. 2016: Subscriptions are now required to access HumanCyc. For more information on obtaining a subscription, click here: http://www.phoenixbioinformatics.org/biocyc#product-biocyc-subscription

Pfam Protein Families

Pfam

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<<<!!!<<< Pfam data and new releases are available through InterPro https://www.re3data.org/repository/r3d100010798 The Pfam website now serves as a static page with no data updates. All links below redirect to the closest alternative page in the InterPro website. >>>!!!>>>

Broad GDAC Firehose

Genome Data Analysis Center

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Born of the desire to systematize analyses from The Cancer Genome Atlas pilot and scale their execution to the dozens of remaining diseases to be studied, GDAC Firehose now sits atop terabytes of analysis-ready TCGA data and reliably executes thousands of pipelines per month. More information: https://broadinstitute.atlassian.net/wiki/spaces/GDAC/

BIGG Database

Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions

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BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

BioCyc Genome Database Collection

formerly: BioCyc Database Collection

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The BioCyc database collection of Pathway/Genome Databases (PGDBs) provides a reference on the genomes and metabolic pathways of thousands of sequenced organisms. BioCyc PGDBs are generated by software that predict the metabolic pathways of completely sequenced organisms, predict which genes code for missing enzymes in metabolic pathways, and predict operons. BioCyc also integrates information from other bioinformatics databases, such as protein feature and Gene Ontology information from UniProt. The BioCyc website provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. From 2016 on, access to the EcoCyc and MetaCyc databases will remain free. Subscriptions to the other 7,600 BioCyc databases will be available to institutions (e.g., libraries), and to individuals. Access to licensed databases via: https://biocyc.org/Product-summary.shtml.

GENCODE

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GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants” by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.