Molecular Biology Research Tools

3D-ALI - Database relating Proteins Structures and Sequences (see Documentation) at EMBL-Heidelberg
AA Composition - Protein Identification in SwissProt using Amino Acid Composition at ExPASy, Switzerland
AA Similarity - Compare the Amino Acid Composition of a SwissProt Entry with Other Entries at ExPASy, Switzerland
BLAST - Basic Local Alignment Research Tool at NCBI
BLITZ at EMBL-Heidelberg
CATH Protein structure classification at UCL-London,
Codon Usage - Codon usage analysis at
Darwin - Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences at ETH-Zürich, Switzerland
dbEST - Database of Expressed Sequence Tags at NCBI (W3)
DBGET - Integrated Database Retrieval System (w/ diagram links) at GenomeNet, Japan (W3)
DOTUP - Dotplot comparison of a DNA sequence with itself at Institut Pasteur
EMNEW - Index of New EMBL Sequences at EBI, UK (W3)
EMP Compound and EMP Pathways - Selkov Enzyme and Metabolic Pathway (EMP) Database at NIH (W3)
EMP Metabolic Pathways - Navigation in Metabolic Pathways from MCS-Computational Biology at Argonne National Laboratory (W3)
ENTREZ - Protein and Nucleotide Database (see Documentation) at NCBI (W3)
ENZYME - The Enzyme Data Bank at ExPASy, Switzerland (W3)
EPD - Eucaryotic Promoter Database at EMBL-Heidelberg, Germany and EPD !New! at GenomeNet, Japan (W3)
EPO !New! - European Patent Office Nucleotide Database at BiO/U. Oslo, Norway (W3) and EPO at CSC, Finland (Gopher)
FASTA - Compare a Nucleic Acid Sequence to Nucleotide Sequence Databases (w/ updates) at EBI, UK, FASTA !Recent! at EERIE-Nimes, France and FASTA !New! at CRIHAN, France (W3)
FlyBase !New! - Genetic and Molecular Database for Drosophila at Harvard U. (W3)
FSSP - Database of Families of Structurally Similar Proteins derived from PDB at EMBL-Heidelberg (W3)
FTHOM !Recent! - Compare Protein Domain Homology at ABC, Hungary (W3)
GDB - Human Genome Data Base at John Hopkins (W3)
GenBank Database (+Updates) at NCBI and GenBank-Fetch at Washington U. (W3)
Gene Finder !New! - Predict Gene Structure, Internal Exons and Splicing Sites in DNA and Exon-Exon Junstion in cDNA at GenoBase at NIH (W3)
Genome Databases !Recent! and Genome Centers !Recent! - World Wide Links at EERIE-Nimes, France (W3)
Genome Workstation !New! - Genome Related Links at Roslin Institute, UK (W3)
Genomic Maps - Links to Genome Specific Resources at Biotech-Indiana (W3)
GenQuest - Search Against Protein Databases with the Q server at John Hopkins (W3)
Grail !New! - Analysis of the Protein Coding Potential of a DNA Sequence (see Documentation) at ORNL (W3)
GSDB - Genome Sequence Database at NCGR (W3)
GuessProt - Selects SwissProt proteins given pI and Mw at ExPASy, Switzerland (W3)
HHS - SwissProt and PDB Systematic Sequence Classification Database at Washington U. (W3)
HOVERGEN !Recent! - Database of Homologous Vertebrate Genes at CAOS/CAMM, The Netherlands (W3)
HSSP - Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at EMBL-Heidelberg (W3)
Kabat - Database of Proteins of Immunological Interest at John Hopkins (Gopher)
Kinemage-Index - "Kinetical Images" by Protein Type at Protein Science (W3)
Klotho - Biochemical Compounds Declarative Database at Washington U. (W3)
LALIGN !Recent! - Calculates the N-Best Local Alignments Between Two Sequences at EERIE-Nimes, France (W3)
LFASTA !Recent! - Local Similarity Searches Between Two Sequences Showing Local Alignments at EERIE-Nimes, France (W3)
LIGAND - Ligand Chemical Database for Enzyme Reactions at GenomeNet, Japan (W3)
LiMB - Listing of Molecular Biology Databases at NIH (Gopher) and LiMB at EMBL-Heidelberg (W3)
Map !Recent! - Restriction Analysis and Translation of a DNA Sequence at EERIE-Nimes, France (W3)
MassSearch - Search SwissProt or EMBL Databases by Protein Mass After Digestion at ETH-Zürich, Switzerland (W3)
Metabolic Database !Recent! - Metabolic Reactions and Pathways at CGSC-Yale U. and Metabolic Database !Recent! at INRA-Moulon, France (W3)
MGD - Mouse Genome Database at Jackson Laboratory (W3)
MHCPEP - Database of Major Histocompatibility Complex (MHC) Binding Peptides at WEHI-Melbourne, Australia (Gopher)
Molecules R US - Interactive Text and Images of PDB Files at NIH (W3)
MPBD - Molecular Probe Data Base at EMBL-Heidelberg (W3) and MPDB at U. Agricultural Sciences, Sweeden (Gopher)
MOOSE !New! - Macromolecular Object Oriented Search Engine to Extract PDB Contained Information at Columbia U. (W3)
MSA - Multiple Sequence Alignment at Washington U. (W3)
MOTIF !Recent! - Search Patterns in Protein Sequences at GenomeNet, Japan Motif at GenomeNet, Japan w/ search from Iowa State (W3)
NDB - Nucleic Acid Database at Rutgers U. (W3)
nnPredict - Predict Protein Secondary Structure at UCSF w/ search from Iowa State (W3)
NRL_3D - Sequence/Structure Database derived from PDB at John Hopkins and NRL_3D at EMBL-Heidelberg (W3)
NRSub !New! - A Non-Redundant DNA Sequence Database for Bacillus subtilis at National Institute of Genetics, Japan (W3)
NuclPepSearch - Search SwissProt for a Nucletide Sequence at ETH-Zürich, Switzerland (W3)
OMIM - Online Mendelian Inheritance in Man at John Hopkins (W3)
Organelle Genome !New! - A Sequence Database at U. Montreal (Gopher)
Organisms and Strains - Links to Databases Specific to Organism and Cell Collections at Biotech-Indiana (W3)
OWL - Non-Redundant Protein Sequence Database (Updated Daily) at John Hopkins (W3)
PDD !New! - Protein Disease Database at NIMH-NCI (W3)
PDB-Browser, PDB-Index and PDB-Pending - Protein Data Bank Structures at Brookhaven National Laboratory, PDB at GenomeNet Japan, PDB at U. Genova, Italy, PDB-List and PDB-Annotated at Brussels Free U., Belgium and PDB-Select at EMBL-Heidelberg (W3)
PDB At A Glance - Hierarchic Access to PDB Files at NIH (W3)
PDBFINDER - A Database Containing PDB, DSSP and HSSP Information (see Documentation) at EMBL-Heidelberg (W3)
PDBSTR - Re-organized Protein Data Bank at GenomeNet, Japan (W3)
PepPepSearch - Search SwissProt for a Peptide Sequence at ETH-Zürich, Switzerland (W3)
PHD - Predict Protein Secondary Structure at EMBL-Heidelberg w/ search from Iowa State (W3)
PHILIP-Bootstrapping Analysis !Recent! - Divergence Between Protein or Nucleotide Sequences at Institut Pasteur, France (W3)
Phospepsort !New! - Digest Phosphorylated Peptide Sequences at EERIE-Nimes, France (W3)
pI/Mw - Compute the Theoretical pI and Molecular Weight of a Protein Sequence at ExPASy, Switzerland (W3)
Pileup !Recent! - Align Protein or Nucleotide Sequences at EERIE-Nimes, France (W3)
PIR - Protein Identification Resource Database at John Hopkins (W3)
PIRALN - Database of Sequence Alignments based on PIR at EMBL-Heidelberg (W3)
PMD - Protein Mutant Database at GenomeNet, Japan and PMD at EMBL-Heidelberg (W3)
PMOTIF - Search Protein Motifs in Gene Sequence at U. Minnesota (W3)
Poland - Calculate the Thermal Denaturation Profile of Double Stranded RNA or DNA at Uni-Düsseldorf, Germany (W3)
PredictProtein !Recent! - Predict Protein Secondary Structure at EMBL-Heidelberg (W3)
PRF - Protein Research Foundation Sequence Database at GenomeNet, Japan (W3)
Primer Selection - Select Primers in a Gene Sequence at U. Minnesota (W3)
PRINTS !Recent! - Protein Motif Fingerprints Database (see Documentation) at EMBnet-Basel, Switzerland (W3)
ProDom - A Protein Domain Database and ProDom-Search at Sanger Centre, UK, ProDom at EMBL-Heidelberg and ProDom-Info at Iowa State (W3)
ProLink - Integrated Database of Protein Structure, Sequence Homology, and Functional Pattern Information at BMERC (Gopher)
PROPSEARCH - Protein Sequence Search for Structural Homology Based on Aminoacid Properties at EMBL-Heidelberg (W3)
PROSITE - Protein Sites and Patterns Database at ExPASy, Switzerland and PROSITE-Search !Recent! at EMBL-Heidelberg (W3)
Protein-Extras at EMBL-Heidelberg (FTP)
Protein Families - Links to Information on Different Protein Families at Iowa State (W3)
Protein Motions !New! - DataBase of Protein Movements at Stanford U. (W3)
PSORT !Recent! - Predict Protein Sorting Signals Coded in Amino Acid Sequences at GenomeNet, Japan (W3)
PSSP !New! - Protein Secondary Structure Prediction at PUU - Protein Domains Database Based on PDB-Select at EMBL-Heidelberg (FTP)
RDP !New! - Ribosomal Database Project at U. Illinois (W3)
ReBase !New! - Restriction Enzyme Database at New England Biolabs, ReBase at EMBL-Heidelberg and ReBase at John Hopkins (W3)
RNA Secondary Structures - Information on Group I Introns and rRNA at U. Colorado-Boulder (W3)
rRNA !New! - Databases of Ribosomal Subunit RNA Sequences at U. Antwerp, Belgium (W3)
SBASE - Library of Protein Domains and SBASE-Search at ICGEB-Trieste, Italy (W3)
SCANPS - Scan Protein Sequences at U. Oxford, UK (W3)
SCOP - Structural Classification of Proteins at Cambridge, UK and SCOP at U. South Florida (W3)
Sequence Annotation - Annotations on NCBI Sequences at Sequence Translation - Translate Gene Sequences at U. Minnesota (W3)
Sleuth - Amino Acid Conformation and Solvent Accessibility of PDB Files at Washington U. (FTP)
SOPM !New! - Self Optimized Prediction Method for Prediction of Protein Secondary Structure at IBCP-CNRS, France (W3)
SRSWWW - Network Browser for Databanks in Molecular Biology (w/ diagram links) at EMBL-Heidelberg (W3)
SRSWWW-Directory !Recent! - Directory of SRSWWW Network Browsers for Biological Databanks and SRSWWW-Global Status !Recent! at EMBnet-Basel (W3)
SSEARCH !Recent! - Universal Sequence Comparison Using the Smith-Waterman Algorithm at EERIE-Nimes, France (W3)
SSPRED !New! - Predict the Secondary Structure of Proteins at EMBL-Heidelberg, Germany (W3)
SURVOL !New! - Analysis of Protein Atomic Volumes at UCMB, Belgium (W3)
Swiss-2DPage - Two-dimensional Polyacrylamide Gel Electrophoresis Database at ExPASy, Switzerland (W3)
SWISSDOM - SwissProt Entries in a ProDom Map at EBI, UK (W3)
Swiss-Model - Automated Protein Modelling at ExPASy, Switzerland (W3)
SWISSNEW - New SwissProt Sequences at EBI, UK (W3)
SwissProt - Protein Sequence Database (+ Weekly Updates) at ExPASy, Switzerland (W3)
Swiss-Shop - Automated SwissProt and Prosite Information Queries at ExPASy, Switzerland (W3)
TBASE !Recent! - Transgenic/Targeted Mutation Database at John Hopkins (W3)
TFASTA !Recent! - Match a Protein Sequence Against All Six Frames of GenBank Sequences at EERIE-Nimes, France (W3)
TFD - Transcription Factor Database at NIH (Gopher)
TFFACTOR and TFSITE - Transcription Factor Data at EMBL-Heidelberg (W3)
Tm - Oligonucleotide Melting Point Determination at U. Minnesota (W3)
TMAP - Identification of Transmembrane Segments on a Protein Sequence at EMBL-Heidelberg (W3)
TMBASE - Transmembrane Protein Database at U. Lausanne, Switzerland (FTP)
Translate !Recent! - Translate a Nucleotide Sequence into Amino Acid Sequence at EERIE-Nimes, France (W3)
TreeGen - Tree Generation from Distance Data at ETH-Zürich, Switzerland (W3)
TREMBL - Database of Translated Peptide Sequences of All CDS Features from EMBL Sequences at EMBL-Heidelberg (W3)
VecBase !Recent! - Cloning Vector Sequence CAOS/CAMM, The Netherlands (W3)
VECTOR !Recent! - Cloning Vector Database at BEN, Belgium (W3), Vector at John Hopkins and Vector-ig at IVR, Kyoto-U., Japan (Gopher)
WebLogo - Sequence Logo Generation at Cambridge U., UK (W3)
SequeOriginally compiled by Pedro M. Coutinho at Iowa State University.