ST NetWatch: Bioinformatics Resources

BRC - Pharmabase 

This NIH funded database has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds. Registered users can access detailed information about various pharmacological compounds. The database is also browseable and searchable.

(Free Site)

BioPAX : Biological Pathways Exchange 

The BioPAX site offers extensive documentation and developmental plans for BioPAX, an open-source represention of metabolic pathway information. Available at the site are user guides, a tutorial, a sizable list of presentation PDFs, a document repository, and a basic roadmap for the software. BioPAX's developers encourage feedback by encouraging users to join a disussion list. They also provide full access to the project's past, present and future plans for development.

(Free Site)

Biological Abstraction Layer for Simulation Analysis (BALSA) 

BALSA is a project of the Cell Systems Initiative of the University of Washington. BALSA is a symbolic language for representing biological processes, including cell signaling. One of the examples includes the canonical Wnt/beta-catenin Pathway from STKE. BALSA is currently a prototype of a Java-based cell systems modeling environment prototype. A cursory explanation of BALSA and its support software, Bioglyphics, can be found on the presentation poster, which is available for view. Additional information can be obtained from Paul Loriaux.

(Free Site)

Biology Workbench 

Maybe you ought to think twice before you buy that bioinformatics package. After all, there are some pretty sophisticated tools freely available on the web. At the Biology Workbench, The San Diego Supercomputing Center brings you free access (with registration) to a range of on-line databases and bioinformatics tools. At the Biology Workbench you can import your own sequence or search multiple databases in one operation and download sequences of interest. Then you'll be able to edit and manipulate your sequences and select from over 30 Protein Tools, over 20 Nucleic Tools, and 10 Alignment Tools. There is no need to worry about file format compatibility and controlling multiple interfaces. That's done behind the scenes leaving you with a single, relatively simple point-and-click interface. (Hint: if you're faced with a bewildering array of buttons, click the banner at the top to toggle to a more informative menu display.) The Workbench will even store your data, ready for your next session. A tutorial with material particularly suited to educators is available at the Biology Workbench Investigation Portal (http://peptide.ncsa.uiuc.edu/).

(Free Site)

Biomolecular Object Network Database (BOND) 

A database of the molecular interactions among proteins. Although, the database is not fully populated yet, the project intends to provide information about molecular interactions, complexes, and pathways from references to 3-D structure to experimental conditions defining interactions. The web interface for data submission and identification of information available in the database was changed September 2004.

(Free Site)

Cancer Genome Anatomy Project (CGAP) 

This site, which is part of the National Cancer Institute's Cancer Genome Anatomy Project, provides a series of interconnected modules that allow access to all CGAP data, bioinformatic analysis tools, and biological resources. The stated goal is "to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment for the patient." The pathways module utilizes the pathways from BioCarta and KEGG (Kyoto Encyclopedia of Genes and Genomes). Each protein encoded by a human gene in a BioCarta pathway and each human enzyme in a KEGG pathway is then linked to its CGAP Gene Info page, and each intermediary metabolite in the KEGG pathways is linked to a CGAP Compound Info page. The SAGE Geie module contains various tools for querying information about human and mouse gene expression profiles in normal and cancerous tissues and cell lines. The SAGE anatomic viewer allows users to view the relative expression of a given gene in normal and malignant tissues of the human body. The output is an intuitive visual display and the queries can be performed using keywords and gene names, which are automatically mapped to SAGE or SNP tags. The RNAi section allows users to search for and map onto the target gene interfering RNAs that can be used for silencing specific genes. The output is user friendly and easy to understand.

(Free Site)

CellML 

CellML is an XML-based markup language being developed by the Bioengineering Institute at the University of Auckland. CellMl is being developed to facilitate the storage and exchange of computer-based mathematical models, including biological models. CellML incorporates existing languages including MathML and RDF to encode mathematical information. The site provides an extensive repository of viewable pathway models, a number of different tutorials and best practice guides, and free downloads of CellML-supporting tools.

(Free Site)

DAVID: Database for Annotation, Visualization and Integrated Discovery 

DAVID provides online functional annotation tools for the analysis of lists of genes and may be especially useful in interpreting microarray data and high-throughput proteomics data. The site was created and is maintained by investigators at the National Institute of Allergy and Infectious Diseases, NIH. Lists of genes are available on the site to demo the functionality. Some of the annotation uses cryptic labels, however help is available with each of the tools and the FAQ section of the technical center provides useful information for getting started. The tools rely on information from several public databases for clustering and annotating the genes.

(Free Site)

Database of Interacting Proteins 

An interactive database based on the published data regarding protein-protein interactions that allows you to search for protein partners. Sequences can be tested for reported interacting proteins or searches can be performed using a text interface using keywords or citation information. New cross-referencing feature links to ProLinks, a database with more than 10 million linkages in over 80 genomes. The site is free for non-profit, academic use. Updated February 7, 2004, with a more user-friendly interface.

(Free Site)

DisEMBL Protein Disorder Prediction/Predictor 

DisEMBL is a computational tool for predicting the probability that particular regions within a protein sequence will be disordered (unstructured). Such unstructured regions frequently contain short motifs involved in protein:protein interactions and targeting. Because these regions may also affect protein stability and expression, DisEMBL may be useful in designing protein constructs.

(Free Site)

DrugBank 

A simple search of DrugBank by drug name (the default setting on the search tool) will tell you what biological processes a particular drug affects. More useful for most signaling researchers, however, is the ability to search the site by gene name or sequence to find drugs implicated in a particular signaling pathway. More sophisticated search tools allow users to search the database by chemical structure, formula or molecular weight. The database includes information for many FDA-approved and experimental drugs, biotech drugs, illicit substances and small molecule drugs. DrugBank is supported by Genome Alberta and Genome Canada in cooperation with GenomeQuest, Inc.

(Free Site)

ELM - Eukaryotic Linear Motif resource 

ELM, the Eukaryotic Linear Motif server, provides a resource for predicting small functional sites in eukaryotic proteins, such as those subject to post-translational modification or involved in protein-protein interactions. Putative functional sites are identified by matching their patterns. Context-based rules and logical filters are applied to reduce the incidence of false positives and thereby improve the predictive power of the server.

(Free Site)

EMBL-EBI: European Bioinformatics Institute 

EMBL-EBI provides database searching and DNA and protein analysis tools. There are at least 20 databases ranging from genomic data to protein data (sequences, structures, and domains) to gene expression data. Users may query the database, perform analysis, or upload data through this site.

(Free Site)

Entrez 

One-stop shopping for information regarding sequences, proteins, 3D structures, genomes, taxonomy, and literature. Entrez is an ambitious and powerful front-end to such diverse databases as GenBank, EMBL, DDBJ, PIR, SWISS-PROT, PRF, PDB, RefSeq, and PubMed, produced by the National Center for Biotechnology Information.

(Free Site)

GeneCards 

A searchable database of human genes adminstered by the Weizman Institute and DoubleTwist, Inc. Searches return a summary of the results with access to a more complete record, which may include the chromosome location, protein function, medical relevance, synonyms, links to homologs in model organisms, and much more.

(Free Site)

Jena Library of Biological Macromolecules 

Look up various biological molecules deposited in the Protein Data Bank or the Nucleic Acid Data Bank. The site allows searching by various terms or unique identifiers and provides an integrated result for any biological molecule with structural information, including a visual representation fo the molecule's structure and an interactive molecule viewer based on the JMOL plug in.

(Free Site)

Kyoto Encyclopedia of Genes and Genomes (KEGG) 

Kyoto Encyclopedia of Genes and Genomes (KEGG) is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects. The site does have signal transduction maps that link to the nucleotide and protein sequences for the proteins in the pathways. From there, one can use KEGG's sequence analysis tools to perform a variety of functions such as predicting transmembrane domains or locating consensus motifs. The KEGG project is being undertaken in the Institute for Chemical Research, Kyoto University as part of the Japanese Human Genome Program. (Current version KEGG Release 21.0, January 2002.)

(Free Site)

NetPhos 

One of the tools available from the Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark. Protein sequences can be searched for putative consensus phosphorylation sites. Access is free to academic users.

(Free Site)

NetworKIN 

More than 500 human kinases and thousands of phosphorylation sites have now been identified. It’s been difficult, however, to determine exactly which protein phosphorylation sites are substrates for which kinases based on information on consensus motifs alone. The NetworKin site uses an algorithm that combines predictions of kinase families likely to phosphorylate particular motifs with contextual information on substrates and kinases to predict which kinases mediate phosphorylation of specific sites. Users can conduct searches for the predicted partners of substrates and kinases of interest or can explore interactions by means of the comprehensive map of the human phosphorylation network.

(Free Site)

PIR - Protein Information Resource 

The February 2002 update indicates that the Protein Information Resource (PIR) contains more than 800,000 entries. PIR is a collaborative effort among the Munich Information Center for Protein Sequences (MIPS), the Japanese International Protein Sequence Database (JIPID), and the National Biomedical Research Foundation. The site provides access and tools for analyzing protein sequence data.

(Free Site)

PlantsP 

This site is devoted to information about phosphorylation in plants. The search interfaces are easy to use and the results for motif searching are customizable, allowing you to only display those results you deem relevant.

(Free Site)

Protein Disorder/Globularity/Domain Prediction 

GlobPlot is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. It successfully identifies inter-domain segments containing linear motifs, and also apparently ordered regions that do not contain any recognised domain. GlobPlot may be useful in domain hunting efforts. The plots indicate that instances of known domains may often contain additional N- or C- terminal segments that appear ordered. Thus GlobPlot may be of use in the design of constructs corresponding to globular proteins, as needed for many biochemical studies, particularly structural biology. GlobPlot has a pipeline interface - GlobPipe - for the advanced user to do whole proteome analysis.

(Free Site)

Protein Kinase Substrate Prediction 

This very easy to use site allows one to ask if your protein is a kinase, what kind, what are the consensus residues that allow the classification, and then allows the user to test for possible substrates based on the predicted phosphorylation consensus motif. You can also use a known kinase to then ask if a test protein sequence can be a substrate for that kinase. The software is Javascript and only runs using Internet Explorer and the text could use a little proofreading, but the interface is extremely easy to use and the output is easy to interpret.

(Free Site)

Robetta Server 

The Robetta server provides automated computational tools for predicting and analyzing protein structures. For structure prediction, sequences submitted to the server are parsed into predicted domains and structural models are generated using comparative modeling if PSIBLAST or fold recognition methods detect a confident match to a protein of known structure, or ab initio structure prediction using the Rosetta fragment insertion method if no match is found. Other capabilities include predicting the effects of mutations on protein-protein interactions (computational alanine scanning).

(Free Site)

SRS 6 at EBI 

The European Bioinformatics Institute's publicly accessible implementation of SRS (tm) Version 6.0 -- a commercial data retrieval system attempting to provide a unified interface for searching and browsing over 300 publicly accessible databases in molecular biology and genome analysis. Not for the faint of heart -- the user interface can be somewhat complex to master (though certainly less complex than mastering 300 separate interfaces!). User discretion is advised: we judge the databases included to range from the authoritative and timely to the quirky and outdated.

(Free Site)

SenseLab 

Senselab contains databases and tools that provide insight into neuronal processes using the olfactory system as a model. There are three neuronal databases and two olfactory databases with tools for analysis. Some of the databases require the Neuron simulation software be installed. Others are more traditional annotated gene and sequence databases. The information tends to be easily browsable and clearly presented.

(Free Site)

SigPath 

SigPath is an information management system designed to support quantitative studies on the signaling pathways and networks of the cell. The system is web-based and allows users to submit and edit information directly about reactions, molecules and their measured concentrations, pathways and quantitative models. Reactions can be assembled into models and exported to a variety of modeling tools, including SBML-compliant tools. SigPath is an open-source bioinformatics project. Details about how to interact with SigPath are described in an STKE Protocol.

(Free Site)

Systems Biology Markup Language (SBML) 

SBML is an XML-based language for representing models of biochemical reaction networks, including signaling pathways, in computer-readable format. STKE has chosen an SBML-compatible file format for machine-readable versions of the Connections Maps database. The website provides assistive documents, schemas, and presentations, as well as a comprehensive FAQ list and two SBML discussion forums. Other highlights are an extensive model repository and a community-editable SBML Wiki area, where users can describe their own experiences with the software and make suggestions for future development. SBML tools include those for validation, visualization, and conversion of SBML files.

(Free Site)

TRANSFAC 

A database for proteins involved in transcriptional regulation. The newest release of the database is version 5.0. The database and tools are free to non-profit users. The database provides detailed information about transcriptional regulators organized in a variety of ways, that includes structural and sequence information and literature references linked to Medline. Access to Transpath, a limited database of signal transduction pathways, and Cytomer, a database of human and mouse organs and systems, are also provided.

(Free Site)

TRANSPATH Signal Transduction Browser 

TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database [Wingender et al. 2000]. It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal transduction pathways are stored together with information about their interaction and references. All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, Swissprot, EMBL, PubMed and others). Selected pathways are displayed as clickable graphic maps.

(Free Site)

TRRD (Transcription Regulatory Region Database) 

A database of transcriptional regulatory factors and the genes that they regulate. The site includes a "Viewer" that requires a Java plug-in, which allows the transcriptional regulatory region (protein binding sites, promoter, silencer, and enhancer regions) of a gene to be viewed as a map. Some of the "Functionally Important Gene Systems" are becoming dated, but still a useful collection of information.

(Free Site)

The Signaling Gateway 

The Signaling Gateway is a collaborative effort of the University of California San Diego (UCSD) and Nature Publishing Group. The site includes the Molecule Pages, which are created using bioinformatics tools and biochemical data and represent the protein components involved in signal transduction. Presently, bioinformatics tools are being used to build an impressive set of related information from multiple databases about a particular protein as defined by its sequence. In some cases, a scientist has "adopted" the protein and provided a "Mini-molecule" page to accompany the derived data.

(Free Site)

UCSC Genome Bioinformatics 

The UCSC Genome Bioinformatics site contains a number of tools. For example with the Gene Sorter tool all of the members of a gene family in a given species (human, mouse, rat, worm, fly, and yeast) can be found and sorted by homology, expression, chromosome position, or gene ontology (GO) annotation. The genes are linked to pages that provide details such as expression data, alleles, phenotypes, and links to the gene's entry in its model organism database. The site also includes tools for browsing genomes, including the In Silico PCR resource for obtaining predicted product sizes in many species (primates, rodents, sea urchins, flies, and more) based on user-defined primer sequences.

(Free Site)

aMAZE 

aMAZE is a system for representing and analyzing molecular interactions and cellular processes. The project's mission is to provide an efficient system that makes computer analysis ready. The signaling pathways (SigTrans) are presently still in the "Old Light Bench" and will be ported to the "Light Bench" in the near future. The metabolic pathways are not completely available through the "Light Bench" interface.

(Free Site)

iHOP (Information Hyperlinked Over Proteins) 

Search the PubMed literature a new way using this site, which relies on text-mining strategies to find sentences containing a particular protein or gene. The sentences are hyperlinked to interacting proteins or genes and biological function words are also highlighted. Once a search has been performed, the user can then view the abstract containing the sentence of interest, perform various additional searches based on hyperlinked terms in the sentences, or build a network by adding the sentences to a "Gene Model". A "Gene Model" is a custom interaction network based on the sentences selected by the user. By selecting particular sentences to include, all of the interacting proteins or genes mentioned in those sentences will show in this user-defined interaction network. The site is the work of Robert Hoffman.

(Free Site)

miRBase 

miRBase is a useful resource about microRNA (miRNA) for researchers seeking to use these molecules in their own labs. The site comprises three databases and is maintained by the Wellcome Trust Sanger Institute. The "Sequences" section contains a database of published miRNA sequences, their genomic locations and associated annotations. Both the hairpin precursor (miR*) and mature forms of the miRNA are included. The "Targets" section contains a database of computationally defined miRNA target genes. The "Registry" section allows researchers to submit a sequence of a new miRNA that is described in an accepted manuscript for naming and indexing in the miRNA sequence database. The Sequence and Targets databases are searchable through the web interface or available for download.

(Free Site)

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