Molecular Biology Research Tool 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

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)

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)

• 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

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 CoursesProtocolesData AnalysisSoftware for ScienceOther 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)

Courtesy : http://www.fredcobio.wordpress.com/