Protein binding hot spots prediction from sequence only by a new ensemble learning method

• Published in: Amino acids Vol. 49; no. 10; pp. 1773 - 1785
• Main Authors: Hu, Shan-Shan, Chen, Peng, Wang, Bing, Li, Jinyan
• Format: Journal Article
• Language: English
• Published: Vienna Springer Vienna 01.10.2017; Springer Nature B.V
• Subjects: Algorithms; amino acid sequences; Amino acids; Analytical Chemistry; artificial intelligence; Binding; binding proteins; Biochemical Engineering; Biochemistry; Biomedical and Life Sciences; Classifiers; Coding; Computation; Computer applications; Databases, Protein; Drug development; drugs; Ensemble learning; Life Sciences; Machine Learning; Mathematical models; Models, Molecular; Neurobiology; Original Article; prediction; Proteins; Proteomics; Sequence Analysis, Protein - methods; Structural analysis; surface area; Hot spot residue; IBk; Ensemble system
• ISSN: 0939-4451; 1438-2199; 1438-2199
• DOI: 10.1007/s00726-017-2474-6

Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods have been widely used for hot spot prediction through sequence or structure characterization. As the structural information of proteins is not always solved, and thus hot spot identification from amino acid sequences only is more useful for real-life applications. This work proposes a new sequence-based model that combines physicochemical features with the relative accessible surface area of amino acid sequences for hot spot prediction. The model consists of 83 classifiers involving the IBk (Instance-based k means) algorithm, where instances are encoded by important properties extracted from a total of 544 properties in the AAindex1 (Amino Acid Index) database. Then top-performance classifiers are selected to form an ensemble by a majority voting technique. The ensemble classifier outperforms the state-of-the-art computational methods, yielding an F1 score of 0.80 on the benchmark binding interface database (BID) test set.Availability: http://www2.ahu.edu.cn/pchen/web/HotspotEC.htm .