Internet Biology Resources

Protein Databases

Databases

• Dialign - Multiple sequence aligner by segments of homology.
• ENZYME (Swiss) - E.C. Number Search in Switzerland
• HPRD - Human Protein Reference database
• Merops - Peptidase Database
• PDB -Search - Advanced Search of the PDB Database
• PIR - The Protein Identification Resource at NBRF
• SWISS-PROT - Protien Sequence Database in Switzerland
• SWISS-SHOP - EMail Swiss-Prot Server

Homology Searching

• Psi-BLAST - NCBI - PsiBlast Server at NCBI - iterates until no more homologues are found!
• BLITZ - Rapid Detection and verification of protein sequence homology
• BLOCKS - Detection and verification of protein sequence homology
• About Blocks - Information About the Blocks Searches
• FASTA 3.3 - EBI - European Bioinformatics Institute FASTA site. (UK)
• FASTA - Japan - Japanese FASTA server
• Motif - Search for motifs in peptides, structures. (Japan)

Inteins - Protein Splicing

• IADFI - Interactive Analysis Database for Protein Splicing
• InBase - Intein Database at NEB, by Perler
• Mechanism - Protein splicing mechanism

3D Structure of Proteins

• Chime - Software for viewing 3D structures - Free with registration
• Chime Resources - Software for viewing 3D structures - Eric Marz support site
• Cn3D Viewer - Download the Cn3D Helper Application for viewing 3D structure files
• NCBI-Structure - 3D Structure Analysis and Viewing
• OMM - Online Macromolecular Museum 3D Structure Viewing.
• PredictProtein - The PredictProtien Server Mirror at Columbia University
• PredictProtein - The PredictProtien Server at EMBL
• Protein Explorer (RasMol) - Software for viewing 3D structures on your Mac or PC screens.

Multiple Sequence Alignment (Protein)

• AllAll - Related Peptide Sequences Database
• BoxShade - Online Multiple Sequence Alignment Printing Tool
• ClustalW - Multiple Sequence Alignment Program at Baylor
• ClustalW - Multiple Sequence Alignment Program at the Pasteur Institute
• ClustalW - ClustalW - (Washington University)
• ClustalX - Download ClustalX For the Mac - Graphical interface.

Pattern Searching

• KinasePhos - A web tool for identifying proteinkinase-specific phosphorylation sites
• MnM - The Minimotif Miner; Finds potentially functional sequence motifs in proteins.
• PATSCAN - Search Genbank for matches to Peptide Sequence Patterns
• PEST - Search for sequences targeting a protein for proteolysis
• PROSITE - Protein Sequence Motifs Database in Switzerland
• SBASE Protein Domain Database

Protein-Protein Interactions

• BIND - Biomolecular Interaction Network Database / Mt. Sinai - Toronto
• DIP - Database if Interacting Proteins from UCLA
• List - GenomeWeb List of Protein Interaction Databases
• PathCalling - Yeast Protien-Protein Interaction Database

Protein Sequence Editing

• AA-Converter - Interconvert 1- and 3-letter amino acid sequences
• SAPS - Statistical Analysis of Protein Sequences (EMBOSS)
• TransSeq - Translate nucleic acid sequence to protein sequence (EMBOSS)