title: A quantitative structure-activity relationship (QSAR) study on glycan array data to determine the specificities of glycan-binding proteins.
abstract: Advances in glycan array technology have provided opportunities to automatically and systematically characterize the binding specificities of glycan-binding proteins. However, there is still a lack of robust methods for such analyses. In this study, we developed a novel quantitative structure-activity relationship (QSAR) method to analyze glycan array data. We first decomposed glycan chains into mono-, di-, tri- or tetrasaccharide subtrees. The bond information was incorporated into subtrees to help distinguish glycan chain structures. Then, we performed partial least-squares (PLS) regression on glycan array data using the subtrees as features. The application of QSAR to the glycan array data of different glycan-binding proteins demonstrated that PLS regression using subtree features can obtain higher R(2) values and a higher percentage of variance explained in glycan array intensities. Based on the regression coefficients of PLS, we were able to effectively identify subtrees that indicate the binding specificities of a glycan-binding protein. Our approach will facilitate the glycan-binding specificity analysis using the glycan array. A user-friendly web tool of the QSAR method is available at http://bci.clemson.edu/tools/glycan_array.
authors.affiliation: School of Computing, Clemson University, Clemson, SC 29634, USA.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Xuan
authors.forename: Yuehua
authors.initials: Y
authors.lastname: Zhang
authors.forename: Tzuen-rong Jeremy
authors.initials: TR
authors.lastname: Tzeng
authors.forename: Xiu-Feng
authors.initials: XF
authors.lastname: Wan
authors.forename: Feng
authors.initials: F
authors.lastname: Luo
mesh_terms: D000465:Algorithms; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009862:Online Systems; D037121:Plant Lectins / Q000737:chemistry*; D011134:Polysaccharides / Q000737:chemistry*; D011485:Protein Binding; D021281:Quantitative Structure-Activity Relationship; D012044:Regression Analysis; D012984:Software
chemical_list: D037121:Plant Lectins; D011134:Polysaccharides