title: A novel method for quantitatively predicting non-covalent interactions from protein and nucleic acid sequence.
abstract: Biochemical interactions between proteins and biological macromolecules are dominated by non-covalent interactions. A novel method is presented for quantitatively predicting the number of two most dominant non-covalent interactions, i.e., hydrogen bonds and van der Waals contacts, potentially forming in a hypothetical protein-nucleic acid complex from sequences using support vector machine regression models in conjunction with a hybrid feature. The hybrid feature consists of the sequence-length fraction information, conjoint triad for protein sequences and the gapped dinucleotide composition. The SVR-based models achieved excellent performance. The polarity of amino acids was also found to play a vital role in the formation of hydrogen bonds and van der Waals contacts. We have constructed a web server H-VDW (http://www.cbi.seu.edu.cn/H-VDW/H-VDW.htm) for public access to the SVR models.
authors.affiliation: School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, PR China.
authors.forename: Jiansheng
authors.initials: J
authors.lastname: Wu
authors.forename: Dong
authors.initials: D
authors.lastname: Hu
authors.forename: Xin
authors.initials: X
authors.lastname: Xu
authors.forename: Yan
authors.initials: Y
authors.lastname: Ding
authors.forename: Shancheng
authors.initials: S
authors.lastname: Yan
authors.forename: Xiao
authors.initials: X
authors.lastname: Sun
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012044:Regression Analysis; D017422:Sequence Analysis, DNA / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods; D013329:Structure-Activity Relationship; D060388:Support Vector Machine
chemical_list: D000596:Amino Acids; D004268:DNA-Binding Proteins; D011506:Proteins; D012313:RNA; D004247:DNA