dorsal/arxiv
View SchemaPredicting Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence
| Authors | Akira R. Kinjo, Ken Nishikawa |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0501015 |
| URL | https://arxiv.org/abs/q-bio/0501015 |
Abstract
Residue-wise contact order (RWCO) is a new kind of one-dimensional protein structures which represents the extent of long-range contacts. We have recently shown that a set of three types of one-dimensional structures (secondary structure, contact number, and RWCO) contains sufficient information for reconstructing the three-dimensional structure of proteins. Currently, there exist prediction methods for secondary structure and contact number from amino acid sequence, but none exists for RWCO. Also, the properties of amino acids that affect RWCO is not clearly understood. Here, we present a linear regression-based method to predict RWCO from amino acid sequence, and analyze the regression parameters to identify the properties that correlates with the RWCO. The present method achieves the significant correlation of 0.59 between the native and predicted RWCOs on average. An unusual feature of the RWCO prediction is the remarkably large optimal half window size of 26 residues. The regression parameters for the central and near-central residues of the local sequence segment highly correlate with those of the contact number prediction, and hence with hydrophobicity.
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"abstract": "Residue-wise contact order (RWCO) is a new kind of one-dimensional protein\nstructures which represents the extent of long-range contacts. We have recently\nshown that a set of three types of one-dimensional structures (secondary\nstructure, contact number, and RWCO) contains sufficient information for\nreconstructing the three-dimensional structure of proteins. Currently, there\nexist prediction methods for secondary structure and contact number from amino\nacid sequence, but none exists for RWCO. Also, the properties of amino acids\nthat affect RWCO is not clearly understood. Here, we present a linear\nregression-based method to predict RWCO from amino acid sequence, and analyze\nthe regression parameters to identify the properties that correlates with the\nRWCO. The present method achieves the significant correlation of 0.59 between\nthe native and predicted RWCOs on average. An unusual feature of the RWCO\nprediction is the remarkably large optimal half window size of 26 residues. The\nregression parameters for the central and near-central residues of the local\nsequence segment highly correlate with those of the contact number prediction,\nand hence with hydrophobicity.",
"arxiv_id": "q-bio/0501015",
"authors": [
"Akira R. Kinjo",
"Ken Nishikawa"
],
"categories": [
"q-bio.BM"
],
"title": "Predicting Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence",
"url": "https://arxiv.org/abs/q-bio/0501015"
},
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