title: Compound analysis via graph kernels incorporating chirality.
abstract: High accuracy is paramount when predicting biochemical characteristics using Quantitative Structural-Property Relationships (QSPRs). Although existing graph-theoretic kernel methods combined with machine learning techniques are efficient for QSPR model construction, they cannot distinguish topologically identical chiral compounds which often exhibit different biological characteristics. In this paper, we propose a new method that extends the recently developed tree pattern graph kernel to accommodate stereoisomers. We show that Support Vector Regression (SVR) with a chiral graph kernel is useful for target property prediction by demonstrating its application to a set of human vitamin D receptor ligands currently under consideration for their potential anti-cancer effects.
authors.affiliation: Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan. jbbrown@sunflower.kuicr.kyoto-u.ac.jp
authors.forename: J B
authors.initials: JB
authors.lastname: Brown
authors.forename: Takashi
authors.initials: T
authors.lastname: Urata
authors.forename: Takeyuki
authors.initials: T
authors.lastname: Tamura
authors.forename: Midori A
authors.initials: MA
authors.lastname: Arai
authors.forename: Takeo
authors.initials: T
authors.lastname: Kawabata
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
mesh_terms: D000465:Algorithms; D000818:Animals; D000970:Antineoplastic Agents / Q000737:chemistry / Q000494:pharmacology; D001185:Artificial Intelligence; D019295:Computational Biology; D016208:Databases, Factual; D015195:Drug Design; D004441:Ecdysterone / Q000819:agonists; D006801:Humans; D008024:Ligands; D021281:Quantitative Structure-Activity Relationship; D018167:Receptors, Calcitriol / Q000378:metabolism; D013237:Stereoisomerism; D013256:Steroids / Q000737:chemistry / Q000378:metabolism; D014807:Vitamin D / Q000031:analogs & derivatives
chemical_list: D000970:Antineoplastic Agents; D008024:Ligands; D018167:Receptors, Calcitriol; D013256:Steroids; D014807:Vitamin D; D004441:Ecdysterone