2005/01/12 by Akira R. Kinjo, Ken Nishikawa, Kinjo, Akira R. +1
Biochemistry, Genetics and Molecular Biology · #Biomolecules (q-bio.BM) #FOS: Biological sciences #Machine Learning in Bioinformatics #Protein Structure and Dynamics #RNA and protein synthesis mechanisms #q-bio.BM
paper · pdf · doi:10.48550/arxiv.q-bio/0501015
22 pages, 5 figures, 2 tables, manuscript submitted
arxiv created 2005/01/12 · openalex publication_date 2005/01/12 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.