Research Tool Sites for Molecular Biology

I’ve added a new link to the Web Links page which contains a large number of links to other useful Molecular Biology web sites.  I would suggest you bookmark it for future reference

Research Tool Sites for the Molecular Biology

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My Favorite Sites

• Essential Research Tools
  • Tools for the Molecular Biology – Quick Access Table
  • EMBOSS – a graphical user interface to the EMBOSS suite of bioinformatics tools. : EMBOSS (European Molecular Biology Open Software Suite) is a suite of free software tools for nucleotide and protein sequence analysis
  • All-IN-ONE SEQ-ANALYZER – by Naohiro Inohara
  • The CMS Molecular Biology Resource – by Christopher M. Smith at SDSC
  • DNA & Protein Analysis Toolkit – Computing Services at The Rockefeller University (USA)
  • JaMBW – Java based Molecular Biologist’s Workbench
    • List of Java-based Molecular Biology Work Bench sites
  • ExPASy Proteomics tools – at Swiss Institute of Bioinformatics (SIB)
  • Research Tools: [FRAME] – by Jun Ishikawa at National Institute of Health (Japan) : You can select [NONFRAME]: [JAPANESE-NONFRAME]
• DataBases
  • GenomeNET: Institute for Chemical Research, Kyoto University Human Genome Center: Kyoto, Institute of Medical Science, University of Tokyo: Tokyo (Japan)
  • Restriction Enzyme Database – New England Biolabs, Inc.
• Table
  • Amino Acid Information
  • Codon_usage
  • Periodic table
• Reference Sites
  • Entrez – NCBI Entrez Browser (USA)
  • The Molecular Biologist’s Desk Reference: at NIH: National Institutes of Health (USA)
  • NCBI PubMed – A search tool for accessing literature citations and linking to their full-text versions at publishers’ Web sites – An experimental service of the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM)
  • PaperChase – PaperChase provides 9,337,834 references – MEDLINE | HealthSTAR | AIDSLINE | CANCERLIT
  • ingenta – Reference search and document delivery service
  • Chemfinder – Chemical Searching and Information Integration
• Others
  • Frontiers in Bioscience: [ THE VIRTUAL LIBRARY ] [ THE JOURNAL ] – The most informative Web-space
  • Schizosaccharomyces pombe & Yeast Sites

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World-Wide-Web Sites

• All the Virology – by the Garry Laboratory in the Department of Microbiology and Immunology in the School of Medicine at Tulane University (USA)
• The Biotechnology Information Center – One of ten information centers at the National Agricultural Library of the US Department of Agriculture: ARS
• Computional Biology and Informatics Laboratory – at Pennsylvenia University
• Computational Molecular Biology: by the Computational Molecular Biology Section (CMBS) at NIH (USA)
• DNA Information and Stock Center: DISC – National Institute of Agrobiological Resources (Japan)
• EMBnet: The European Molecular biology network: [ http://ben.vub.ac.be/ | ftp://dbmdec5.ulb.ac.be/ | ]
• European Bioinformation Institute (UK)
• The ExPASy Molecular Biology Server – by Amos Bairoch at the Geneva University Hospital and the University of Geneva (Switzerland)
• GenomeNET: Institute for Chemical Research, Kyoto University Human Genome Center: Kyoto, Institute of Medical Science, University of Tokyo: Tokyo (Japan)
• Health Sciences Topics – Molecular Biology: Medical Center at Vanderbilt University (USA)
• Human Genome Center: Institute of Medical Science at The University of Tokyo (Japan)
• Image Library of Biological Macromolecules – featured as website of the day on February 19, 1997 by the ‘webzine’ HMS Beagle.
• MRC – Human Genetics Unit – WWW Server(UK)
• National Institute for Basic Biology: NIBB (Japan)
• Sheffield ChemDex – at University of Sheffield (UK)
• Theoretical Biophysics Group – NIH Resource for Concurrent Biological Computing at Beckman Institute for Advanced Science and Technology
• UK MRC HGMP Resource Centre – Human Genome Mapping Project Resource Centre (UK)
• Weizmann Institute Genome and Bioinformatics: (Israel)

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Useful Database Sites

• ATCC – American Type Culture Collection
• Databases for Molecular Biology – NIH (USA)
• DNA Data Bank of Japan: DDBJ – Center for Information Biology of Genetics – SAKURA On-Line Gene Submission (Japan)
• DSHB: Developmental Studies Hybridoma Bank under the auspices of the National Institute of Child Health & Human Development (USA)
• EMBL DataBase
• Escherichia coli Databank – at The Graduate School of Biological Sciences: NAIST (Japan)
• E.coli Genetic Stock Center: CGSC – E. coli Stock Center Database at Yale University (USA)
• E. coli Genome Project: The purpose of this server is to provide a front-end graphical interface to our FTP site – at University of Wisconsin-Madison (USA)
• GenBank Database
• A Gene Map of the Human Genome – The Gene Map web site is hosted by the National Center for Biotechnology Information: NCBI (USA)
• GenLink – at Washington University (USA)
• Online Research Resources – The National Center for Human Genome Research: Genome and Genetic Data at The National Center for Human Genome Research (NCHGR): The Human Genome Project for the National Institutes of Health (NIH)
• MPDB: The Molecular Probe Data Base – The Molecular Probe Data Base (MPDB) contains information on ca. 4000 synthetic oligonucleotides with a sequence of up to 100 nucleotides – at The Interlab Project (Italy)
• National Collection of Yeast Cultures – at Genetics and Microbiology Department, Institute of Food (UK)
• NDB: Nucleic Acid Database – The goal of the Nucleic Acid Database Project is to assemble and distribute structural information about nucleic acids at The State University of New Jersey (USA)
• REBASE: Restriction Enzyme Database – by Richard J. Roberts
• Restriction Enzyme Information Resources – by Mary Hoenecke and Carolyn Stock at Promega Corporation (USA)
• SEQNET – The U.K. academic communitiesSEQuence NETwork computer for molecular biologists at Daresbury Laboratory (UK)
• TIGR Database- TDB: a collection of molecular biology databases (USA)
• TIGR Human Genome Sequencing Projects – at The Institute for Genomic Research: TIGR (USA)

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• Protein Database and Resources
  • ENTREZ: Protein and nucleotide database (NCBI)
  • ENZYME: Enzyme nomenclature database
  • Molecules R US: Web interface for accessing molecular structure data in PDB
  • ProDom: The ProDom protein domain database consists of an automatic compilation of homologous domains detected in the SWISS-PROT database – The ProDom team in Toulouse (France)
  • PRO-SITE: Dictionary of protein sites and patterns
  • Protein Data Bank: Brookhaven National Laboratory
  • PROLYSIS: A protease and protease inhibitor Web server by Thierry MOREAU (France)
  • SCOP: Structural Classification of Proteins. Release 1.32. 4432 PDB Entries (all through May 96). 8330 Domains. 169 Literature References. – at MRC Laboratory (UK)
  • SWISS-PROT: Annotated protein sequence database

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Research Protocol & Tool Sites

• To Get More Software: TRY This Page !!
• BioPD – at Interdepartmental Biological Building – University of Padova (Italy) 05.5.21
• BOXSHADE 3.21 – Pretty Printing and Shading of Multiple-Alignment files – by the Bioinformatics Group at the ISREC (Swiss Institute for Experimental Cancer Research) in Epalinges s/Lausanne
• Computational Biochemistry Research – at ETH: Eidgenossische Technische Hochschule Zurich
• FramePlot.pl: v.0.5 – coding region prediction of high G+C-content bacteria by Jun Ishikawa at National Institute of Health (Japan)
• Genome Information Research Center: Home Page in Japanese – at Osaka University (Japan)
• A Guide to Structure Prediction (version 2)
• IDEAS – Integrated Database and Extended Analysis System for Nucleic Acids and Proteins – at GenomeNET (Japan)
• Molecular Biology Club – Biology Courses|Protocoles|Data Analysis|Software for Science|Other Sotware…
• Molecular Phylogenetic Tree – Making Molecular Phylogenetic Tree at Kyoto University (Japan)
• Multiple Alignment Resource – VSNS BioComputing Division (Germany)
• NIH Image Home Page – The most powerful “Image” soft
• PCR Methods
  • Long PCR Protocol
  • PCR Jump Station – The ultimate Web page for information and links on all aspects of the Polymerase Chain Reaction (PCR)
  • Primer3: Pick PCR primers from nucleotide sequence by Steve Rozen and Helen J. Skaletsky at Whitehead Institute for Biomedical Research (USA)
• Molecular Biology Protocols
• Search the Genentech Web Site – Genentech, Inc.
• SOSUI – Secondary Structure Prediction of Membrane Proteins at GenomeNET (Japan)