Bioinformatics Resources and Tools

The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center, whose goals are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community.

BeeBase is a comprehensive sequence data source for the bee research community. It currently hosts the genomes of Apis mellifera and three of its pathogens, as well as Bombus terrestris and B. impatiens; the genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.

FlyBase is an online bioinformatics database and the primary repository of Drosophila Genes & Genomes. The data types include mutant phenotypes, molecular characterization of mutant alleles and other deviations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions.

MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. The projects contributing to this resource are:Mouse Genome Database (MGD) Project; Gene Expression Database (GXD) Project; Mouse Tumor Biology (MTB) Database Project; Gene Ontology (GO) Project at MGI; MouseMine Project

PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.

The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.

VectorBase is an NIAID Bioinformatics Resource Center dedicated to providing data to the scientific community for Invertebrate Vectors of Human Pathogens. VectorBase contains a variety of data types, including reference and variant genome sequence, structural annotations (e.g., gene models, protein domains), functional annotations, and phenotypic and population data for traits such as insecticide resistance.

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.

Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research.

ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community.

The microRNA.org website is a comprehensive resource of microRNA target predictions and expression profiles.

A collection of miRNA expression profiles in human cancers. These are automatically extracted from literature published on PubMed before being manually curated post-extraction to ensure data is accurate. Search by cancer names or use the on-site sequence analysis tools.

miRDB is an online database for miRNA target prediction and functional annotations. All the targets in miRDB were predicted by a bioinformatics tool, MirTarget.

miRWalk provides a large and freely accessible archive of predicted and validated miRNA-target interactions. miRNA binding sites within the complete sequence of the gene are documented, along with experimentally verified miRNA-target interaction data collated from four other existing resources.

Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services.
These tools are classified according to their application field, trying to cover the whole drug design pipeline.

This website provides: (1) e-Drug3D: Search the FDA approved drugs either by keyword or by substructure. (2) De novo drug design: Invent ideas of ligand (scaffold-hopping) by the de novo drug design program LEA3D. (3) Combinatorial library design: Build combinatorial library of molecules. (4) Screening / Docking: Virtually screen and dock small molecules into the structure of a target protein. (5) Build a molecule: Draw a molecule by using the ACD applet (v.1.30) or the MarvinSketch (v5.9.0) and generate 3D coordinates by using the program Frog.

This website provides access to our knowledgebase of molecular replacements, useful for compound optimization in drug design.

This website provides an access to: (1) SwissDock, a web service to predict the molecular interactions that may occur between a target protein and a small molecule; (2) S3DB, a database of manually curated target and ligand structures, inspired by the Ligand-Protein Database.

This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.

SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins.

This website allows you to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280'000 compounds active on more than 2000 targets of 5 different organisms.

Given a small molecule which can be drug, drug candidate, natural product, or new synthetic compound, TarFisDock docks it into the protein targets in PDTD (Potential Drug Target Database), and outputs the top 2%, 5% or 10% candidates ranked by the energy score, including their binding conformations and a table of the related target information.

BioBase Biological Databases, A QIAGEN® Company, provides HGMD® Human Gene Mutation Database, TRANSFAC® Transcription Factor Binding Sites, POSSUMweb - Pictures Of Standard Syndromes and Undiagnosed Malformations, ANNOVAR™, The PharmacoGenomic Mutation Database (PGMD™), BRENDA - The Enzyme Database

A growing repository of the vast array of databases and online tools in the field of biology and it's sub-disciplines. Includes extended descriptions of each resource and links to tutorials.