title: Computational methods for identification of functional residues in protein structures.
abstract: The recent accumulation of experimentally determined protein 3D structures combined with our ability to computationally model structure from amino acid sequence has resulted in an increased importance of structure-based methods for protein function prediction. Two types of methods for function prediction have been proposed: those that can accurately predict overall biochemical or biological roles of a protein and those that predict its functional residues. Here, we review approaches used for the computational identification of functional residues in protein structures and summarize their applications to a wide variety of problems in functional proteomics, such as the prediction of catalytic residues, post-translational modifications, or nucleic acid-binding sites. We examine four different problems in order to perform a comparison between several recently proposed methods and, finally, conclude by identifying limitations and future challenges in this field.
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.
authors.forename: Fuxiao
authors.initials: F
authors.lastname: Xin
authors.forename: Predrag
authors.initials: P
authors.lastname: Radivojac
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry* / Q000502:physiology; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D000596:Amino Acids; D011506:Proteins