Many programs exist for, e.g.,
- Prediction of physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.).
- Detection of repetitive protein sequences.
- Statistical analysis of protein sequences.
- Prediction of coiled coil regions in proteins (different methods).
- Identification of PEST regions.
- Prediction of peptide binding.
- Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.).
- Representations of a protein fragment as a helical wheel.
Located on the ExPASY server are:
- ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.).
- Compute pI/Mw - Compute the theoretical pI and Mw from a SWISS-PROT or TrEMBL entry or for a user sequence.
- ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.).
- RandSeq - Random protein sequence generator.
Example: Using ProtParam, Compute pI/Mw, ProtScale and RandSeq for the analysis of SWISS_PROT Accn.no P35523.
- Enter the Accession no into the query box for Acc.no. and hit Submit.
- ProtParam: What are the Parameters of the potential extracellular domain (aa 858-988) of the protein?
- Compute pI/Mw: What are the Parameters of the potential extracellular domain (aa 858-988) of the protein?
- ProtScale: View the Hphobhobicity plot according to Kyte & Doolittle (default) with a Window size of 21. Click Sumbit on the next page again. Can you predict the number of transmembrane spanning domains (very hydrophobic regions) using this tool? (12 tms)
- RandSeq: Change the radio button from average amino acid composition (default) to Composition of a specific sequence and enter your SWISS-PROT/TrEMBL ID P35523. Click Submit. A random sequence will be generated.
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