Bioinformatics sites:
Many companies and research institutes currently provide a wealth of public data for the bioinformatics researcher. We have compiled some of the more useful sites. We try to keep the links current, but if there is a problem or comment, please feel free to contact us at:
contactus@bio-balance.com

Areas of Bioinformatics:

Computational Biology

http://cbcsrv.watson.ibm.com/Tspd.html
IBM Bioinformatics Group - Tools & Content

http://www.bindingdb.org/bind/index.jsp
The BindingDB is a public, web-accessible database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds.The database currently contains data generated by isothermal titration calorimetry (ITC) and enzyme inhibition (Enz. Inhib.) methods; other techniques will be included in the future.

http://www.cbrc.jp/index.eng.html
1) Establishment of Mathematical Models as a Foundation of Bioinformatics Research and development of mathematical theories and algorithms such as probabilistic models, and of advanced storage, retrieval, and deduction systems for biological information, as a common foundation for bioinformatics research.
2) R&D of Technologies for Finding Gene Regions in Large Genome Sequences and Predicting Protein Functions; Development of comprehensive and high-speed analytical techniques for determining genes in genome sequences accurately and for predicting structure and function of proteins coded by genes.
3) R&D of Protein-structure Prediction Technologies through the Convergence of Statistical Information and Physical-energy Computations; Development of computational techniques for predicting the 3D structure of proteins by combining physical-energy calculations with statistical knowledge, and of techniques for estimating 3D structure based on image processing technologies.
4) R&D of Technologies for Simulating Intra-cell Biological Phenomena Development of data-analysis techniques for elucidating intra-cell metabolic networks and genetic-control networks, and development of integrated simulation systems for those networks.

http://x.amath.unc.edu:16080/BioNetS/
BIOchemical NETwork Stochastic Simulator (BioNetS): Software for Stochastic Modeling of Biochemical Networks

http://www.cs.sunysb.edu/~algorith/
The Stony Brook Algorithm Repository

Proteomics and Structural Biology:
http://www.rcsb.org/pdb/index.html
Welcome to the PDB, the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.

http://www.pir.uniprot.org/
Welcome to UniProt UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProt is comprised of three components, each optimized for different uses. The UniProt Knowledgebase (UniProt) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Non-redundant Reference (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences. The sequences and information in UniProt are accessible via text search, BLAST similarity search, and FTP.

http://gibk26.bse.kyutech.ac.jp/SMS/index_t_mirror.html
SMS (Sting Millenium Suite) is a web-based, publicly-available software, developed to aid researches in their quest for translating information about the structures of macromolecules into knowledge.

http://dip.doe-mbi.ucla.edu/
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.

http://www.chem.qmw.ac.uk/iubmb/enzyme/
Enzyme Nomenclature Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzyme-Catalysed Reactions

Molecular Pathways

http://www.biocarta.com/genes/allpathways.asp
BioCarta - All Pathways Observe how genes interact in dynamic graphical models. Our online maps depict molecular relationships from areas of active research. In an "open source" approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species. Find both classical pathways as well as current suggestions for new pathways.

http://www.blueprint.org/bind/bind.php
BIND is an expanding database of biomolecular interaction, pathway and complex information. All information is stored in BIND database records that are freely available through a web interface that allows users to query, view, and submit records. The Biomolecular Interaction Network Database (BIND) is a database designed to store full descriptions of interactions, molecular complexes and pathways. The BIND database is freely available to both academics and commercial researchers. Please click on the links at the bottom of this page to view our policies. BIND contains interaction, molecular complex and pathway records.

http://www.signaling-gateway.org/
The AfCS-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction. This Gateway represents a unique collaboration between academia and scientific publishing and is designed to facilitate navigation of the complex world of research into cellular signaling. Information and data presented here are freely available to all.

http://www.brenda.uni-koeln.de/
The Comprehensive Enzyme Information System

http://doqcs.ncbs.res.in/~bhalla/doqcs/template.php?x=links&y=index
Links to other resources for databases and simulators of signaling pathways

Genetics and Genomics
http://www.genome.gov/
The National Human Genome Research Institute led the Human Genome Project for the National Institutes of Health, which culminated in the completion of the full human genome sequence in April 2003. See also: http://www.genome.gov/Research/

http://www.tigr.org/
The Institute for Genomic Research

http://www.ncbi.nlm.nih.gov/genomes/Complete.html
NCBI list of completely sequenced genomes
see also: http://www.ncbi.nlm.nih.gov//entrez/query.fcgi?db=Genome

http://pedant.gsf.de/
Genomes database

http://www.kazusa.or.jp/java/codon_table_java/
A nice codon table applet in Java gives usage frequencies for all different species.

http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml
A beginner's guide to the human genome project from Oak Ridge National Laboratory The Science Behind the Human Genome Project Basic Genetics, Genome Draft Sequence, and Post-Genome Science

http://alces.med.umn.edu/VGC.html
Virtual Genome Center

http://sevens.cbrc.jp/1.20/search.php
We developed an automated system for discovering seven transmembrane helix receptors (7-TMR) in the whole human genome sequences using algorithms of gene finding, sequence search, motif and domain assignment, transmembrane helix prediction and the gene quality refinement. This system is intended to detect sequences of multi-exon or remote homologues that can not be detected by using conventional sequence search tools alone. With the careful assessment of the analyzing components, we obtained candidate datasets, with several predicting accuracy, among which we found at least 1,032 and at most 1,700 candidate 7-TMR genes from human genome.

http://www.genome.ad.jp/about_genomenet/
GenomeNet is a Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology.

http://www.nslij-genetics.org/wli/
The Robert S. Boas Center for Genomics and Human Genetics

http://www.thearkdb.org/about.html
About ARKdb The ARKdb database system provides comprehensive public repositories for genome mapping data from farmed and other animal species, providing a resource similar in function to that offered by GDB or MGD for human or mouse mapping data respectively. Data stored includes details of loci and markers, references/papers, authors, genetic linkage map assignments, cytogenetic map assignments, experimental techniques, PCR primers and conditions and any other data pertaining to genome mapping. The data is entered by curators assigned to the individual species and funded by grant funding from a variety of sources. For details of the curators and editors for a particular species database, please refer to the links listed on the species list page.The system is entirely web-operable and can be queried for textual information (e.g. locus details, papers from a particular author etc.) or for graphical map displays. The maps are drawn using the Anubis map viewer using data extracted from the database "on the fly". Multiple maps can be displayed at once and compared, either within or between species.

http://www.informatics.jax.org/
Mouse Genome Informatics
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.

http://gdb.jst.go.jp/gdb/gdbtop.html
The Genome Database

General Sites
http://cellbiol.com/index.php
the Bio-Web
Many Bioinformatics tools

http://molbiol-tools.ca/
More Bioinformatics tools

http://www.ncbi.nlm.nih.gov/Entrez/
Entrez, The Life Sciences Search Engine

http://www.dur.ac.uk/biological.sciences/Bioinformatics/bioinformatics_corner.htm
This site provides a collection of useful links to gateways to WWW sites providing information, software (on-line or for download) and other useful facilities.

http://amdec-bioinfo.cu-genome.org/html/index.html
Bioinformatics - New York State - Large Scale Computing Introduction - The Facility offers a comprehensive set of tools and databases for everything from quick special projects to large scale sequence analysis and software development.

http://www.amdec.org/
AMDeC Foundation, Inc. (AMDeC) seeks to establish New York as an international center for biomedical research and technology. AMDeC's thirty-nine affiliated institutions include New York's pre-eminent medical schools, academic health centers, and other research institutions. Through AMDeC, these institutions are working collaboratively to develop large-scale basic science and clinical research projects, genomics core facilities, and to otherwise expand New York's research infrastructure.

http://gibk26.bse.kyutech.ac.jp/jouhou/jouhoubank.html
BioInfo Bank

http://genome.wustl.edu/
The Genome Sequencing Center at Washington University Medical School focuses on the large scale generation and analysis of DNA sequence. We play a leadership role in The Human Genome Project , constructing the clone map and contributing 25% of the finished sequence. To better understand the human genome sequence and to advance the study of biology, we also have sequenced the genomes of other species as can be found in these pages. The open sharing of genomics methodology and the rapid release of sequence data via our website serves to empower other researchers and facilitates the elucidation of gene function, forming the ultimate basis for an understanding of how DNA sequence dictates the form and function of an organism, both in health and in disease.

http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html National Center for Biotechnology Information Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources

http://www.pcbi.upenn.edu/
University of Pennsylvania Center for Bioinformatics

http://www.cbi.pku.edu.cn/
Welcome to CBI - the Centre of BioInformatics at Peking University . As the national node of the European Molecular Biology Network (EMBnet) and the Asia Pacific Bioinformatics Network (APBioNet), we provide bioinformatics resource and service for Chinese biologists, including DNA and protein sequence database and protein structure database, software tools for database query and database search, as well as bioinformatics news, documents and user manuals (more...)

http://www.tree.caltech.edu/
Caltech Genome Research Laboratory

http://arep.med.harvard.edu/
Harvard-Lipper Center for Computational Genetics

http://www.ebi.ac.uk/
The European Bioinformatics Institute (EBI) is a non-profit academic organisation that forms part of the European Molecular Biology Laboratory (EMBL).The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.The mission of the EBI is to ensure that the growing body of information from molecular biology and genome research is placed in the public domain and is accessible freely to all facets of the scientific community in ways that promote scientific progress.

http://www.utyx.com/bioinformatics/

http://www.healthtech.com/genomelink.asp
CHI gathers information through the organization of scientific conferences, publication of market reports, and compilation of industry deals. We would like to share some of the information we have gathered with you. The following articles offer insight into the Life Science industry. We hope you find this information useful.

Bioinformatics News
http://www.ebi.ac.uk/Information/News/news.html