Complete table of available documents

ExPASy
What's New on ExPASy SWISS-FLASH electronic bulletins How to create HTML links to services on ExPASy Disclaimer Complete description of the ExPASy proteomics Web server [PDF file]

Databases	Tools and Software Packages
Swiss-Prot - Protein sequences User manual & release notes General documents Nomenclature documents Species specific documents Other documents PROSITE - Protein families and domains User manual & release notes List of documentation entries Syntax of PROSITE patterns Generalised profile syntax SWISS-2DPAGE - Two-dimensional polyacrylamide gel electrophoresis User manual & release notes Protocols ENZYME - Enzyme nomenclature User manual & release notes SeqAnalRef - Sequence analysis bibliographic references User manual & release notes Electronic mail addresses of authors cited	SRS, Sequence retrieval system Swiss-Shop: automatically obtain (by email) new sequence entries relevant to your field(s) of interest Protein identification and characterization AACompIdent - Identify proteins with amino acid composition AACompSim- Compare the amino acid composition of a Swiss-Prot entry with all other entries MultiIdent - Identify proteins with pI, Mw, amino acid composition, sequence tag and peptide mass fingerprinting data TagIdent - Identify proteins with pI, Mw and sequence tag, or generate a list of proteins close to a given pI and Mw PeptIdent - Identify proteins with peptide mass fingerprinting data, pI and Mw FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses FindPept - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage. PeptideMass - Calculate masses of peptides and their posttranslational modifications for a Swiss-Prot or TrEMBL entry or for a user sequence PeptideCutter - Predict potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence Compute pI/Mw - Compute theoretical pI and Mw from a Swiss-Prot or TrEMBL entry or for a user sequence Pattern and profile searches ScanProsite - Scan a sequence against PROSITE or a pattern against Swiss-Prot and TrEMBL Primary structure analysis ProtParam - Physico-chemical parameters of a protein sequence (composition, extinction coefficient, etc.) ProtScale - Amino acid scale representation (hydrophobicity, other conformational parameters, etc.) Tertiary structure Swiss-PdbViewer - An automated knowledge-based protein modelling server SWISS-MODEL - A program to analyse and superimpose protein 3D structures PTM prediction The Sulfinator - Prediction of tyrosine sulfation sites Alignment SIM - Local similarity program LALNVIEW - A graphical viewer for pairwise alignments 2-D PAGE Melanie - Software package for 2-D PAGE analysis Make2ddb - A package preparing the data and the programs necessary to build a federated 2-DE database on one's own web site Guidelines for building a federated 2-DE database

Databases

Tools and Software Packages

Swiss-Prot - Protein sequences
PROSITE - Protein families and domains
SWISS-2DPAGE - Two-dimensional polyacrylamide gel electrophoresis
- User manual & release notes
- Protocols
ENZYME - Enzyme nomenclature
- User manual & release notes
SeqAnalRef - Sequence analysis bibliographic references
- User manual & release notes
- Electronic mail addresses of authors cited

SRS, Sequence retrieval system
Swiss-Shop: automatically obtain (by email) new sequence entries relevant to your field(s) of interest
Protein identification and characterization
- AACompIdent - Identify proteins with amino acid composition
- AACompSim- Compare the amino acid composition of a Swiss-Prot entry with all other entries
- MultiIdent - Identify proteins with pI, Mw, amino acid composition, sequence tag and peptide mass fingerprinting data
- TagIdent - Identify proteins with pI, Mw and sequence tag, or generate a list of proteins close to a given pI and Mw
- PeptIdent - Identify proteins with peptide mass fingerprinting data, pI and Mw
- FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides
- GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses
- FindPept - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage.
- PeptideMass - Calculate masses of peptides and their posttranslational modifications for a Swiss-Prot or TrEMBL entry or for a user sequence
- PeptideCutter - Predict potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence
- Compute pI/Mw - Compute theoretical pI and Mw from a Swiss-Prot or TrEMBL entry or for a user sequence
Pattern and profile searches
- ScanProsite - Scan a sequence against PROSITE or a pattern against Swiss-Prot and TrEMBL
Primary structure analysis
- ProtParam - Physico-chemical parameters of a protein sequence (composition, extinction coefficient, etc.)
- ProtScale - Amino acid scale representation (hydrophobicity, other conformational parameters, etc.)
Tertiary structure
- Swiss-PdbViewer - An automated knowledge-based protein modelling server
- SWISS-MODEL - A program to analyse and superimpose protein 3D structures
PTM prediction
- The Sulfinator - Prediction of tyrosine sulfation sites
Alignment
- SIM - Local similarity program
- LALNVIEW - A graphical viewer for pairwise alignments
2-D PAGE
- Melanie - Software package for 2-D PAGE analysis
- Make2ddb - A package preparing the data and the programs necessary to build a federated 2-DE database on one's own web site
- Guidelines for building a federated 2-DE database

Last modified 22/Jan/2003 by ELG

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