I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following :
- Length of peptide
- Number of Each Amino Acid
- Percent composition of each amino acid
- Molecular weight
- Net charge of peptide
- Positive charge
- Negative charge
- Isoelectric point (pI)
- Hydropathicity
- Percent polar amino acids
- Percent positive amino acids
- Percent negative amino acids
- Percent hydrophobic amino acids
- Hydrophobicity
- Lipophilicity
- Amphiphilicity
- Water-Octanol Partition Coefficient
- Steric Bulk
- Side chain bulk
- Net donated hydrogen bonds
- Percent alpha helix
- Percent random coil
- Percent beta sheet
While some of these properties are self explanatory ( eg. size, num. of amino acids, percentage of amino acids. ) and easy to compute. Other properties ( like Molecular weight, Net. charge, Positive charge, Hydorphobicity etc ) have been difficult for me.
I donot have Chemistry or Biology background and hence have found these difficult to compute. I would be appreciative if someone could point me in the correct direction ( I have already been through Wikipedia ) containing methods to compute the above mentioned properties or to a standard text which would explain the above mentioned properties and also provide methods to compute them. Thank you all.
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