Computational Chemistry and Biology Databases

ExPASy      Access Swiss-Model Automated Protein Modelling Server, Prosite databases etc

The PIMM Force Field

The 20 amino acids

The PROMISE Database home page

Brookhaven Protein Data Bank

Database of drugs

Many organic molecules from Canada

MathMol Molecular Library

The RCSB Protein Data Bank

NDB - The Nucleic Acid Database

Families of Structurally Similar Proteins (FSSP) database -- database of structural alignments of proteins found in the PDB

NCBI HomePage

CCDC Products

The Cambridge Structural Database System

CAMBRIDGE DATABASE Table of Contents

LIPIDAT

IMB Jena Image Library of Biological Macromolecules

Chemical DATA

NIST Chemistry WebBook

Reduction Potentials compilation by Peter Wardman

Gaussian Basis Set Order Form

NCSA ChemViz (Cambridge Database and more)

Sequence Database Searching

Combined Databases
Nucleic Acid Databases
Protein Databases
Database Notification Services
Image Databases
Miscellaneous Databases
Database Indexes
Database Sources (downloadable images of sequence databases)
Organism-Specific Databases

Sequence Analysis
Journal Indexes
Journals

Other Electronic Publications
Associations and Publishers
Software
Indexes of BioScience-Related Services
Molecular Biology www Servers
Granting Agencies
Educational Resources, Short Courses, and Problem sets
Miscellaneous

Sequence Database Searching

Combined Databases

• ATLAS (PIR/EMBL/GenBank/EMBL/SwissProt)
• BLAST (GenBank/EMBL/SwissProt/PIR)
• BLAST2 at EMBL (GenBank/EMBL/SwissProt/PIR) 
• ISREC BLAST (GenBank/GenPept/dbEST/dbSTS/EMBL/SwissProt/PIR/TIGR + others)
• Maestro GDSB (DDBJ/EMBL/GSDB/NCBI databases)
• WWW-Query (EMBL/Genbank/NRSub/Hovergen/HIDB)
• SRS EBI (SwissProt/PIR/EMBL/TREMBL/Prosite/BLOCKS/Medline/Rebase/DBEST + others)

Nucleic Acid Databases

• DNA Data Bank of Japan
• Genbank (text keyword search)
• GenBank (search by species)
• GSDB - Genome Sequence Database
• Nucleic Acid Structure Database

Protein Databases

• SWISS-PROT (Protein database)
• Molocules-R-Us PDB (NIH)
• PDB (Brookhaven)
• PIR (NBRF)
• PIR FASTA search (MIPS)
• Protein structure predection database
• SRS EBI (SWISS-PROT/PIR/EMBL/TREMBL/Prosite/BLOCKS)

Database Notification Services
notifies you of additions to databases with homology to your sequence

• ALERT (PIR/EMBL/GenBank/EMBL/SwissProt)
• Sequence Alert System
• SWISS-Shop (SwissPROT)

Image Databases

• EMBL Virus Structures
• Image Library of Biologial Macromolecules
• Molecules-R-Us (NIH)
• SWISS-3DIMAGE Annotated 3-D Images
• Visulation of Viruses (U of Wisconson)

Miscellaneous Databases

• AAA Protein Superfamily database
• ACUTS (Ancient Conserved Untranslated Sequences)
• Androgen Receptor Gene Mutation Database
• Cell Line Database
• CCSD(CarbBank) - Complex Carbohydrate Structural Database
• COPE - Cytokines Online Pathfinder Encyclopaedia
• dbCFC - Cytokine Family EST database
• dbEST (database of Expressed Sequence Tags)
• Database of Genome Sizes (DOGS)
• dbSTS (database of Sequence Taged Sites)
• DBGET (Integrated Database Retrieval System)
• Enzyme nomenclature Database
• GENBANK codon useage database
• GOBASE - Organelle Genome Database
• Haemostasis Research Group Database
• HIC-Up - Hetero-compound structural Database
• HIV Molecular Immunology Database
• HIV Protease Database
• HotMolecBase (Molecules with Medical Applications)
• IMGT - Immune System Recognition Genome Database
• Internet Biodiversity Database
• LIPIDAT
• Molecular Probe Database
• MOOSE Macromolecular Structure Database
• Mouse Knockout and Mutation Database
• NLGIP - Nat. Lab. for Genetics of Isralei Population
• Obsolete PDB entries (San Diego Supercomputer Center)
• PDB 3D structure browser (Brookhaven Nat. Lab.)
• Netherlands Culture Collection of Bacteria
• PROMISE (PROsthetic groups and Metal Ions in protein active SitEs)
• Protein Motions Database
• PKR - Protein Kinase Resource
• RELIBase - Receptor/Ligand structural database
• RHdb - Radiation Hybrid Database
• Ribosomal Database Project
• SRPDB - Signal Recognition Particle Database
• TRANSFAC - Transcription Factor Database
• TransTerm - Translational Signal database
• Vector Sequence Database

Database Indexes

• DBCAT - Index of Molecular Biology Databases

Database Sources (downloadable images of sequence databases)

• Human STS - Human Physical Mapping Project, Whitehead Institute
• Mycobacterium tuberculosis Open Reading Frames
• PIR (NBRF)
• PRINTS (UK) protein motif fingerprint database 
• TREMBL Translated protein sequence database, EBI

Organism-Specific Databases

• Mammalian 
  • CEPH - Human Genotype Database 
  • Human Chromosome 1 Database
  • Human Chromosome 13 Database
  • Human Chromosome 22 Database
  • Human Genome Project Database 
  • Mouse Genome Database
  • Human Mitochondrial Genome database
  • Portable Dictionary of the Mouse Genome
• Worm 
  • Caenorhabditis Genetics Centre (C. Elegans)
  • Filarial GenomeNetwork
• Insect 
  • Arabinet (AtDB)
  • Mosquito Genomics
• Yeast 
  • Saccharomyces Protein Structural Info
  • Saccharomyces cerevisiae Genome Database
• Fungi 
  • Aphyllophorales Taxonomic Database
  • Filamentous Fungi Database
• Prokaryote 
  • CBS/NCC Bacteria Database
  • E.coli Genetic Stock Center 
  • Non-Redundant Bacillus subtilis Database
• Viral 
  • HIV Sequence Database
  • HPVSD - Human Papillomavirus Sequence Database
  • World Health Organization Malaria Database
• Plant 
  • TIGR - Arabidopsis thaliana database
• Other 
  • Ribosomal Database Project

Sequence Analysis

• ALIGN (Pairwise Sequence Alignment)
• Cytogenetic Correspondence Linkage Map Note: Requires Java-compliant browser
• DAS (Transmembrane Region Prediction)
• FGENE (Gene structure Prediction)
• HPT-Search (Protein Homology Search)
• MatInspector (Locate NA sequence matches in TRANSFAC database)
• Gene-map Homology Search
• Genome Navigator - Interactive Genome Viewer 
• INCA Recursive BLAST database search (Requires Java)
• Multi-Align (Multiple Sequence Alignment)
• NCBI ORF (Open Reading Frame Finder)
• PEDANT - Protein Extraction, Description, and ANalysis Tool
• DNA and Protein Pattern analysis (PBIL)
• Pol3Scan (tRNA/TDNA genes)
• SAPS (Statistical Analysis of Proteins)
• SEALS System for Easy Analysis of Lots of Sequences (NCBI)
• Secondary Structure Prediction
• SeqPup - Sequence Editor and Analysis Note: Requires Java-compliant browser
• ToPLign (Toolbox for Protein Alignments)
• TMpred (Prediction of Transmembrane Regions)
• WebCutter (Restriction Maps) 

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Journal Indexes

• Elsevier Science Journals Table of Contents 
• PubMed - NCBI's MEDLINE service

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Journals

• American Crystallopgraphic Society Newsletter
• Amino Acids
• Analytical Biochemistry
• Ancient Biomolecules
• Annals of Human Genetics
• Antimicrobial Agents and Chemotherapy 
• Applied and Environmental Microbiology
• Archives of Biochemistry and Biophysics
• Archives of Virology
• Autoimmunity 
   
• Biocatalysis and Biotechnology
• Biochemistry
• Bioconjugate Chemistry
• Biochimica et Biophysica Acta Full Issue Set
• BBA - Bioenergetics (non-subscribers - access to TOC only)
• BBA - Biomembranes (non-subscribers - access to TOC only)
• BBA - Gene Structure & Expression (non-subscribers - access to TOC only)
• BBA - General Subjects (non-subscribers - access to TOC only)
• BBA - Lipids and Lipid Metabolism (non-subscribers - access to TOC only)
• BBA - Molecular Basis of Disease (non-subscribers - access to TOC only)
• BBA - Molecular Cell Research (non-subscribers - access to TOC only)
• BBA - Protein Structure and Molecular Enzymology (non-subscribers - access to TOC only)
• BBA - Reviews on Biomembranes (non-subscribers - access to TOC only)
• BRC - Biochemical and Biophysical Research Communications
• Biochemical Education
• Biochemical Journal
• Biochemical Society Transactions
• Biochemical Systematics and Ecology
• Biochimie
• Bioinformatics
• Biology of the Neonate
• Biological Signals and Receptors
• Bioorganic Chemistry
• Biophysical Journal
• Biopolymers
• Biotechnology & Applied Biochemistry (Abstracts Only)
   

  
   
   

• Cancer Biochemistry Biophysics
• Carbohydrate Letters
• Cell (non-subscribers - access to TOC only)
• Cell Adhesion and Communication
• Cellular Physiology & Biochemistry
• Chemistry and Biology
• Chemistry and Physics of Lipids
• Clinical Biochemistry
• Clinical and Diagnostic Laboratory Immunology
• Clinical and Experimental Biochemistry
• Clinical Microbiology Reviews
• Clinical Science
• Comparitive Biochemistry and Physiology
• Current Advances in Protein Biochemistry
• Current Biology (Free Registration Required)
• Current Opinion in Biotechnology (Free Registration Required)
• Current Opinion in Cell Biology (Free Registration Required)
• Current Opinion in Genetics and Development (Free Registration Required)
• Current Opinion in Immunology (Free Registration Required)
• Current Opinion in Neurobiology (Free Registration Required)
• Current Opinion in Structural Biology (Free Registration Required)
• Cytokine 
   

  
   
   

• Electronic Journals in Biology
• EMBO Journal
• European Journal of Biochemistry
• European Journal of Human Genetics (Free Registration Required)
• Experimental Cell Research 
   

  
   
   

• FEBS Letters
• FEMS Microbiology Reviews
• FEMS Immunology & Med. Microbiology
• Structure with Folding & Design (Free Registration Required)
• Fungal Genetics and Biology 
   

  
   
   

• GENE-COMBIS (Computing for Mol. Bio. Information Service)
• Genes & Development
• Genes to Cells
• Genome Research
• Genomics
• Glycobiology
• Growth Factors 
   

  
   
   

• Heredity
• Hormone Research
• Human Heredity
• Human Moleuclar Genetics 
   

  
   
   

• Immunity (non-subscribers - access to TOC only)
• Immunlogy Today
• Infection and Immunity
• International Journal of Bio-Chromatography
• International Journal of Biochemistry & Cell Biology
• International Journal of Biological Macromolecules
• Intervirology 
   

  
   
   

• Journal of the American Chemical Society
• Journal of Applied Crystallography
• Journal of Bacteriology Current Research in Bacteria and Other Organisms (monthly)
• Journal of Biochemical and Biophysical Methods
• Journal of Biochemistry and Molecular Biology
• Journal of Biochemistry, Molecular Biology and BioPhysics
• Journal of Biological Chemistry
• Journal of Cell Biology (TOC Only)
• Journal of Enzyme Inhibition
• Journal of Clinical Microbiology 
• Journal of Immunological Methods
• Journal of Molecular Biology
• Journal of Molecular and Cellular Cardiology
• Journal of Molecular Modeling
• Journal of Organic Chemistry
• Journal of Peptide Research (TOC Only)
• JPSS - Journal of Pharmacy & Pharmaceutical Sciences
• The Journal of Physiology
• Journal of Virology Biochemistry, genetics, structure, immunity of viruses (monthly) 
   

  
   
   
   
   

• Macromolecules
• Medical Biochemistry
• Membrane and Cell Biology
• Methods (Companion to Methods in Enzymology)
• Methods in Enzymology
• Microbiology and Molecular Biology Reviews
• Molecular and Cellular Biology
• Molecular and Cellular Probes
• Molecular Cell (non-subscribers - access to TOC only)
• Molecular Diversity
• Molecular Human Reproduction
• Molecular Vision A Peer reviewed web journal (monthly)
• Molecules and Cells
• Mutation Research
• Mutagenesis 
   

  
   
   

• Nanobiology
• Nature A journal of science (Free registration required - weekly)
• Nature - Biotechnology
• Nature - Medicine
• Nature - Genetics Mammalian, human genetics & the Human Genome Project (Free registration required - monthly)
• Nature - Structural BiologyStructure of biological macromolocules (Free registration required - monthly)
• Nucleic Acids Research Methods, Structural & Molecular Biology, Enzymology
• Nucleic Acid Methods 
   

  
   
   

• Pesticide Biochemistry and Physiology
• Proceedings of the National Academy of Sciences USA
• Progress in Biophysics and Molecular Biology
• Progress in Lipid Research
• Protein Engineering
• Protein Expression and Purification 
   

  
   
   

• Receptors and Channels
• RNA 
   

  
   
   

• ScienceResearch in all areas of science (weekly)
• Seminars in Immunology
• Seminars in Virology
• Soil Biology & Biochemistry
• Structure (Free registration required) 
   
• The Biochemist
• Transgenics
• TIBS - Trends in Biochemical Sciences 
   
• Virology 
   
• World-Wide Web Journal of Biology Peer-reviewed Electronic Journal

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Other Electronic Publications

• ASM News
• The BioInformer (EBI Newsletter)
• HMS Beagle - News about currently published research
• Human Genonme News
• NCBI Newsletter
• Quebec Science
• Technical Tips Online - Techniques for Molecular Biologists

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Associations and Publishers

• Academic Press
• American Association for the Advancement of Science
• American Chemical Society
• American Crystallographic Association
• American Peptide Society
• American Society for Microbiology
• BioMedNet
• Blackwell Science
• Cambridge University Press
• Canadian Society for Biochemistry, Molecular, and Cellular Biology
• Canadian Society for Pharmaceutical Sciences
• Churchill Livingstone
• Cold Spring Harbor Laboratory
• Elsevier Science
• FASEB
• FEMS (Fed. of Eur. MicroBiological Soc.)
• Genetical Society
• Gordon and Breach Publishing Group
• International Union of Biochemistry and Molecular Biology
• International Union of Crystallography
• IOS Press
• Oxford University Press
• Physiological Society
• Portland Press
• The Protein Society
• RNA Society
• Springer Science Online 

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Software

• AcaClone pDRAW32 - Freeware DNA cloning, analysis and visualisation software
• Artemis DNA sequence viewer and annotation tool (Java)
• BioCatalog - Catalog of software for molecular biology and genetics
• BioInformatics Template Library (C++ library)
• DBWatcher - Schedules BLAST search at every DB update
• DNATools - DNA and protein sequence analysis (Win95/98)
• DotMatrix - Dot Matrix Generation Program (Macintosh)
• Dynafit - statistical analysis of (bio)chemical kinetics and equilibrium binding data
• EMBOSS - European Molecular Biology DNA analysis software suite (UNIX)
• ID50 - Calculate inhibitory and infectious doses (IBM | Macintosh)
• GENEDOC - Multiple Sequence Alignment Editor for Windows
• Gepasi - Biochemical Systems Kinetic Simulator
• gOpenMol - GUI for OpneMol Computational Chemistry programs
• LASSAP - Large Scale Sequence Analysis (unix)
• MacVector - new version now available 
• Membrane Protein Explorer(MPEx) and Membrane Topology Database(MPTopo)- exploring the topology and other features of membrane proteins
• MODELER - Homoplogy protein structure modeling (UNIX)
• Molecular Linux - MolBio Software for Linux
• Pence/MRC-Group Software Centre
• PHYLIP - Phylogeny Inference Package
• PlasmidMaker - Plasmid drawing software (Macintosh)
• PRATT - Find patterns in unaligned protein sequences
• ProMSED2 - Protein multiple alignment editor (Win 3.1/95)
• PUZZLE - Maximum likelihood analysis for AA/NA alignments
• Regress+ - non-line curve fitting, deterministic and stocastic modelling (macintosh)
• RNADraw - RNA structure predection (windows/unix)
• Sequencher - Sequence analysis software
• Seqin - Sequence submission tool
• SeqSearch - Primer Design/Motif Search/Restriction mapping (Windows)
• SeqWeb - Web-based Sequence Analysis
• Structural Biology Software Database - University of Illinois
• VacMan - analysis of infectivity data from animal trials (IBM / Macintosh)
• VMD- Visualization and Analysis of Biomolecular Systems (unix/windows)
• WPDB - protein structure database search and display (Win 3.1/95/NT)

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Indexes of BioScience-Related Services

• Amos' WWW links page
• All the Virology Servers in the World
• Art's Biotechnology Resource - links to resources and software
• BeanRef - literature and links to research on beans
• BioCrawler - links in many sections of life sciences
• Biolinks
• Biology Links 
• Genamics Links to molecular biology software, journals, and microbial genome projects 
• Pedro's BioMolecular Research Tools
• Scott's Botanical Links
• US Geological Survey Index of Biology Servers

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Molecular Biology www Servers

• Australian National University Bioinformatics Facility
• Computational Genomic Group (CGG)
• The Cytokines Web
• Expasy Molecular Biology Server
• Harvard Biological Laboratories
• Human Genone Project Information
• HUM-MOLGEN Communication Forum in Human Molecular Genetics
• Institue for Moleuclar Virology (U of Wisconson - Madison)
• National Biotechnology Information Facility (New Mexico)
• Molbio.org Molecular Biology, Biochemistry & Genetics news and discussion groups 
• RNA World
• Virology World Wide Web Server

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Granting Agencies

• Canada 
  • Alberta Heritage Foundation for Medical Research (AHFMR)
  • Alberta Research Council (ARC)
  • Canadian Cancer Society
  • Heart and Stroke Foundation of Canada
  • Medical Research Council of Canada (MRC)
  • Natural Scienes Research Council of Canada (NSERC)
• United States 
  • Centers for Disease Control and Prevention (CDC), Bethesda MD USA
  • National Cancer Institute (NCI)
  • National Institutes of Health (NIH)
  • National Science Foundation (NSF)
  • Whitaker Foundation

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Educational Resources, Short Courses, and Problem sets

• Access Excellence - Biology Teaching & Learning Resources
• The Biology Project Web Biology Course (U of Arizona)
• BIODIDAC Resources for Biology Teaching
• Clinical Case Tutorials in Biochemistry
• Fundamentals of Sequence Analysis (Caltech)
• Immunoassay Animations
• Kimball's Biology Pages - Definitions for Biology
• MendelWeb Mendelian Genetics tutorial

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Miscellaneous

• IBM/Optipat and U.S. Government Patent Searches
• Canadian BioScience Jobs
• Fisher Scientific Catalog
• Image Library of Biological Macromolecules
• Life Sciences Dictionary
• Nobel Prize Internet Archive
• ChemJobs.Net