Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization.
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ABSTRACT:
SUBMITTER: Rajgaria R
PROVIDER: S-EPMC2635923 | biostudies-literature | 2009 Mar
REPOSITORIES: biostudies-literature
Publications
Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization.
Rajgaria R R McAllister S R SR Floudas C A CA
Proteins 20090301 4
A new optimization-based method is presented to predict the hydrophobic residue contacts in alpha-helical proteins. The proposed approach uses a high resolution distance dependent force field to calculate the interaction energy between different residues of a protein. The formulation predicts the hydrophobic contacts by minimizing the sum of these contact energies. These residue contacts are highly useful in narrowing down the conformational space searched by protein structure prediction algorit ...[more]
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