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Wednesday, July 27, 2011

Bioinformatics Research centers and Universities

12:26 AM  Hope  



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List of Bioinformatics Information Databases

12:24 AM  Hope  



  • 2can Bioinformatics Short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators. 
  • Addgene A non-profit organization dedicated to promoting sharing of plasmid constructs described in published literature. Addgene stores original plasmid samples submitted by scientists and distributes them for use in advancing life science research.
  • ALFRED Allele frequency database from the Kidd Lab at Yale Univ.
  • ANGIS Australian National Genomic Information Service provides access for biologists to a comprehensive system of bioinformatics software, databases, documentation, training and support, on a subscription basis.
  • Anti-Cancer Maps Public database with viewing tools (NCI).
  • ARP Antibody Resources Page
  • ATCC American Type Culture Collection
  • Atlas of Side-Chain and Main-Chain Hydrogen Bonding is available for biomolecular modellers (UK)
  • AtlasInfo Bioinformatics System for AtlasTM cDNA Expression Arrays 
  • Bacterial Names with Standing in Nomenclature
  • Base4 Bioinformatics Integrated systems solutions for biotechnology and pharmaceutical development.
  • BCM Search Launcher Baylor Human Genome Center
  • Berkeley Drosophila Genome Project
  • BGEM Mousebrain Gene Expression Map database at St. Jude
  • BIND Biomolecular Interaction Network Database
  • BIOBASE Specialized biological databases, mainly from the field of molecular biology, including the TRANSFAC database on transcription factors, their genomic binding sites and their general binding profiles.
  • BioCarta Proteomics marketplace and resource center.
  • BioChipNet More than 13.000 records on companies and institutions involved in microarray technology microarray-relevant publications, comprehensive glossary, upcoming biochip-related meetings and conferences, and hyper to public databases.
  • bioinf.org.uk Bioinformatics Web Site of Dr. Andrew C.R. Martin.
  • Bioinformatic Harvester Caches and cross-links public bioinformatic databases and prediction servers to provide fast access to protein specific bioinformatic information. Presently the following databases and servers are implemented: Uniprot/SWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI.
  • Bioinformatics Club Bioinformatics resource providing access to widely used bioinformatics databases and tools.
  • Bioinformatics.net Directory of bioinformatics and molecular biology.
  • Bioinformatics.org News and information. Links to online computational tools.
  • Biomax Informatics Bioinformatics software.
  • BioNavigator Tools to manage and analyze the large amounts of data generated by bioscience research.
  • Biosciences databases.
  • BioSimGrid A distributed database for biomolecular simulations.
  • BioTX Automation Design and construction of complex mechanical components; automated liquid handling for the life science laboratory; USGRD database of federal grants awarded.
  • BioWisdom Ontologies and related tools focused on drug discovery. .
  • BRENDA Comprehensive enzyme information system. 
  • California Digital Library Searchlight ... searches databases.
  • CCP11 Project Collaborative Computational Project 11 was established to foster the broad bioinformatics community and the UK research community in particular. Its purpose is to facilitate the transfer of knowledge and expertise through conferences, workshops, a newsletter and the use of the world wide web
  • Chartsbank.com A market research portal with an extensive pharmaceutical pipeline database.
  • Chmoogle Access to millions of public domain chemical structures and information about them; fast substructure searches.
  • CKAAPs DB Contains the analysis of conserved amino acid positions based on protein structural alignment from CE and FSSP; provides an analysis of conserved key positions in protein structures, with implications in structural integrity, functional site or protein engineering studies.
  • Clinical Bioinformatics Ontology "Existing medical vocabularies lack rich terms to describe findings generated by molecular diagnostic and cytogenetic techniques. Likewise, bioinformatics resources were not designed to support the needs of the clinical community. The Clinical Bioinformatics Ontology™ (CBO) was initiated to address these gaps and covers the areas of molecular genetics, molecular pathology, cytogenetics and infectious disease."
  • CPBP The Carcinogenic Potency Database
  • CSH Protocols Cold Spring Harbor - Methods from MolecularCloning.com along with selected protocols from many of our best-selling manuals, such as Cells and Antibodies, as well as protocols from Cold Spring Harbor’s renowned on-site courses. In addition, new cutting-edge protocols submitted by and commissioned from laboratories worldwide. 
  • Database of Macromolecular Movements Includes associated tools for geometric analysis.
  • DataEdge Information to assist in pharmaceutical development, clinical trials and related activities.
  • DBCAT The catalog of databases.
  • DBSubLoc Database of Protein Subcellular Localization at Institute of Bioinformatics, Tsinghua University.
  • Deltagen Bioinformatics - Library of functional information about mammalian gene families with potential relevance to small molecule drug discovery; Gene knockout and conditional knockout programs; discover and identify the functional role of rare or novel secreted proteins.
  • Derwent GENSEQ Information on nucleic and amino acid sequences from worldwide patents.
  • Developmental Therapeutics Program Resources for drug development, including compound libraries, cell lines, screening, and databases.
  • DNA Data Bank of Japan
  • DOE U.S. Department of Energy-sponsored human genome research projects.
  • DrugBank Bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, pathway) information. Contains nearly 4100 drug entries including >700 FDA-approved small molecule drugs, 110 FDA-approved biotech (protein/peptide) drugs, >100 nutraceuticals and >3200 experimental drugs. More than 15,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Users may query DrugBank in any number of ways.
  • DSDBASE Database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein. 
  • EBI European Bioinformatics Institute
  • ELM The Eukaryotic Linear Motif resource for predicting functional sites (described by linear motifs) in eukarytic proteins.
  • Elsevier Scientific BioMedDirect Integrated group of products and services addresses the needs of the biomedical research community and corporate healthcare markets, providing comprehensive navigation and linking to full text.
  • EMBL A service for sequence analysis, and structure prediction
  • EMBL European Molecular Biology Laboratory centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
  • eMOTIF Nucleic acid database.
  • Environmental Mutagen Society
  • First Genetic Trust Secure, web-based technology system for handling and analyzing medical and genetic information.
  • FishBase Global Information System on Fishes 
  • GATC GmbH Sequencing service.
  • GBF Research Group for Bioinformatics The focus of the GBF research group bioinformatics are regulatory genomic signals and regions, in particular those that govern transcriptional control.
  • gdb The Genome Database
  • GeMCRIS NIH Genetic Modification Clinical Research Information System, a comprehensive information resource and analytical tool for scientists, research participants, institutional oversight committees, sponsors, federal officials, and others with an interest in human gene transfer research.
  • Gene and Protein Synonym Database Comprehensive database of gene and protein name synonyms. This authoritative thesaurus, published by PharmaDM, has been compiled in cooperation with SIB (the publishers of Swiss-Prot and ExPASy), OFAI, the University of Manchester, and others.
  • Gene Ontology Project A controlled vocabulary to describe gene and gene product attributes in any organism.
  • GeneGo Develops tools for integration and systems level analysis of high-throughput experimental data in human biology and medicinal chemistry. Includes MetaBase, a manually curated database on human biology in norm and diseases
  • Genetics at Yahoo via Yahoo
  • Genetics Education Center University of Kansas Medical Center
  • Genetics Home Reference The National Library of Medicine's web site for consumer information about genetic conditions and the genes or chromosomes responsible for those conditions.
  • Genetics Section of the WWW Virtual Library
  • Genolist Genome Browser Useful links to genome sequence sites.
  • Genome@home Stanford Univ. grid computing project.
  • GenomeNet Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology.
  • Genomics and Bioinformatics Group NIH Bioinformatic program packages, microarray data analysis information, and molecular databases for genomic and proteomic research.
  • GermOnline A cross-species community annotation knowledgebase that provides microarray data relevant for the mitotic and meiotic cell cycle as well as gametogenesis. Importantly, GermOnline also integrates knowledge about genes important for sexual reproduction that is contributed and updated by members of the scientific community in collaboration with professional curators.
  • Globin Gene Server Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin.
  • GTOP Database Genomes TO Protein structures and functions; constructed by the Laboratory for Gene-Product Informatics at the National Institute of Genetics 
  • HCV Database Hepatitis C
  • HGMD Human gene mutation database
  • HGSC Human Genome Sequencing Center
  • HGVbase Human Genome Variation database (formerly.HGBASE)
  • H-Invitational Database H-Invitational Database (H-InvDB) is a human gene database, with integrative annotation of 41,118 full-length cDNA clones currently available from six high throughput cDNA sequencing projects. (July 2004)
  • HIV Sequence Database
  • Human Genome Mapping Project (HGMP) Resource Centre (UK) A rich source of information and .
  • Human Genome Project
  • Human Genome Variation Society Locus Specific Mutation Databases Out of date but has some good to other variation databases.
  • Human Serum Proteome Human serum proteomic database to provide a reference resource to facilitate and direct future investigations of the vast archive of pathophysiological content in serum.
  • HyperCLDB Detailed descriptions of cell lines from European culture collections 
  • IFPMA Clinical Trials Portal International Federation of Pharmaceutical Manufacturers and Associations clinical trials registry
  • IMGT The international ImMunoGeneTics database, is an integrated database specialising in Immunoglobulins (Ig), T-cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all species.
  • IncyteGenomics Genomic information-based tools to accelerate the discovery and development of new diagnostic and therapeutic products.
  • Informatics Online "Healthcare research and analytic community designed to meet the present and future needs of healthcare researchers and market economics professionals."
  • Inpharmatica Biopendium, a resource of protein structure and function information that enables the identification of distantly related proteins to identify high quality drugable targets and predict the structure of interacting ligands, facilitating the rational design of lead compounds.
  • InterPro Resource for whole genome analysis.
  • ISI A database publisher with a focus on Web-based products that offer scholarly research information in the sciences, social sciences, and arts & humanities, including BioSciences Citation Index, Chem Sciences Citation Index, and Clinical Medicine Citation Index. 
  • KEGG Kyoto Encyclopedia of Genes and Genomics 
  • Leadscope Chemoinformatics software, databases created with the U.S. FDA along with prediction capabilities.
  • Library of Protein Family Cores Taking the structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures. 
  • Mammary Transgene Database The Molecular Biology Computational Resource, Baylor College of Medicine, Houston, Texas
  • MDL Information Systems Discovery informatics for the life sciences and chemistry in industry and academia; a wide variety of software for discovery informatics, high throughput chemistry, biological data management, content browsing and data analysis, chemical sourcing and logistics, bioactivity databases, synthetic methodology, patents, etc.
  • MedDRA MSSO MedDRA Maintenance and Support Services
  • MedGene Database Harvard's database uses an automated approach to assemble disease-gene co-citation matrices from the titles, abstracts and MESH terms of over 11 million Medline records and normalizes these gene-disease relationships into rank order.
  • MHC Haplotype Project A framework and resource for association studies of all MHC linked diseases.
  • MICROMEDEX Knowledgebases for healthcare, safety and the environment.
  • mips Munich Information Center for Protein Sequences.
  • Molecular Toolbox Sidney Morris' collection of databases and utilities.
  • NAPRALERT A relational database of all natural products, including ethnomedical information, pharmacological/biochemical information of extracts of organisms in vitro, in situ, in vivo, in humans (case reports, non-clinical trials) and clinical studies. Similar information is available for secondary metabolites from natural sources.
  • NCBI National Center for Biotechnology Information (USA) Excellent to databases. BLAST NCBI GenBank
  • NCBI Trace Archive Developed to store the raw data underlying all of the sequence generated by the genome project.
  • NCTR National Center for Toxicological Research, US FDA, Center for Toxicoinformatics
  • NDB Nucleic Acid Database at Rutgers
  • NHGRI U.S. National Human Genome Research Institute (U.S.) Software available for download, including ArrayDB, ComboScreen, eSAGE, GeneMachine, G.A.S.P., NHGRI::Blastall.pm perl module, SOOP, WebBlast andothers.
  • NIH Office of Dietary Supplements Extensive dietray supplements information.
  • NOAA Molecular Biology Server / Bioinformatics US Dept Commerce/NOAA/NMFS/NWFSC 
  • Oak Ridge National Laboratory
  • PCR .com Web guide of polymerase chain reaction technique.
  • PDB RCSB Protein Data Bank, worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
  • PDB Protein Data Bank - tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
  • PDBbind Database The public-accessible PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). Most of the binding affinity data (>95%) in the PDBbind database were collected from original references.
  • Pfam Large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
  • Phenomic Database A multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indexes (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene in this database allows the user to compare phenotypes of a gene over many organisms simultaneously.
  • PhRMA Bioinformatics Industry information, meetings, news.
  • pkr Protein Kinase Resource
  • PredictProtein
  • ProClass Database Non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies.
  • ProDom Comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.
  • Profile Scan Server Motif scanning in protein sequences.
  • PROLYSIS A Web resource for those interested in proteases and their natural or synthetic inhibitors; contains informations of general interest as well as useful to other Internet resources.
  • PROSITE Database of protein families and domains; consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs.
  • Protein Information Resource (PIR) In collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain; contains about 2000,000 non-redundant protein sequences.
  • ProtoNet Automatic hierarchical classification of proteins.
  • PubChem Provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative
  • PubGene Data-mining software that searches through the millions of biology-related papers published for the names of all human genes; articles are then searched for the occurrence of gene pairs.
  • PubGene Norway Mirror for PubGene 
  • Reactome A collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology
  • repairGenes Information about DNA repair genes and a useful resource for research on DNA repair.
  • SBASE Online protein domain library.
  • SciFinder A service of the American Chemical Society.
  • SIB Swiss Institute of Bioinformatics
  • Sigma-Aldrich Library of Rare Chemicals
  • SIS (EVCAM) Scientific Information Service on advanced alternative methods to animal experiments in biomedical sciences; a database of the European Commission.
  • Skeletal Muscle Gene Expression Database A centralized source of up to date information regarding the effects of changes in contractile activity on the profile of genes expressed in skeletal muscle.
  • SNP Consortium
  • Stanford Microarray Database SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization. Data is released to the public at the researcher's discretion or upon publication.
  • STD Sequence Databases Specialized databases that are an expansion of the human papillomavirus project funded by the National Institute of Allergy and Infectious Diseases (NIAID).
  • STN Connects scientists and engineers to the world's most complete and authoritative databases; includes AnaVist interactive analysis and visualization software that offers a variety of ways to analyze search results from scientific literature and patents as well as visualize patterns and trends in the research.
  • STRBase Short Tandem Repeat DNA Internet Database at NIST
  • SURFACE Database containing the results of a large-scale protein annotation and local structural comparison project; includes visulaization tools.
  • SWICZ Swiss-Czech proteomics web server created by the Laboratory of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, and Division of Molecular Microbiology, Biozentrum, University of Basel. The aim of this server is presentation of developmental proteomics databases of Caulobacter crescentus, Streptomyces coelicolor and Streptomyces granaticolor. 
  • TAP The Yeast TAP Project is aimed at elucidating the entire network of protein-protein interactions in a model eukaryotic organism, namely the yeast Saccharomyces cerevisiae,
  • The Human Genome Wellcome Trust public information site.
  • TIRC Toxicology Information Response Center
  • TreeBASE A relational database of phylogenetic information. 
  • UBC Bioinformatics Center Univ. of British Columbia, Canada
  • UMC Products WHO Drug Dictionary Enhanced, WHO Herbal Dictionary, international drug safty data, WHO-ART adverse reaction terminology, training in the use of WHO Drug Dictionaries. 
  • Virtual Genome Center
  • Virus databases on-line Research School of Biological Sciences, The Australian National University 
  • WebMol by Dirk Walther (UCSF) A Java PDB (Brookhaven Protein Data Bank) viewer.
  • Wiley's Scientific, Technical, and Medical Databases A range of fee-based databases, including mass spectrometry.
  • WIT What-Is-There? A www-based system to support the curation of function assignments made to genes and the development of metabolic models.
  • wwPDB Worldwide Protein Data Bank - consists of three member organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. 
  • Zebrafish Information Network

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