title: Progress and challenges in predicting protein interfaces.
abstract: The majority of biological processes are mediated via protein-protein interactions. Determination of residues participating in such interactions improves our understanding of molecular mechanisms and facilitates the development of therapeutics. Experimental approaches to identifying interacting residues, such as mutagenesis, are costly and time-consuming and thus, computational methods for this purpose could streamline conventional pipelines. Here we review the field of computational protein interface prediction. We make a distinction between methods which address proteins in general and those targeted at antibodies, owing to the radically different binding mechanism of antibodies. We organize the multitude of currently available methods hierarchically based on required input and prediction principles to provide an overview of the field.
authors.forename: Reyhaneh
authors.initials: R
authors.lastname: Esmaielbeiki
authors.forename: Konrad
authors.initials: K
authors.lastname: Krawczyk
authors.forename: Bernhard
authors.initials: B
authors.lastname: Knapp
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Nebel
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Deane
mesh_terms: D000595:Amino Acid Sequence; D000936:Antigen-Antibody Complex / Q000737:chemistry; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods / Q000639:trends; D030562:Databases, Protein / Q000706:statistics & numerical data; D000939:Epitopes / Q000737:chemistry; D006801:Humans; D021621:Imaging, Three-Dimensional; D000069550:Machine Learning; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs / Q000235:genetics; D025941:Protein Interaction Mapping / Q000379:methods / Q000706:statistics & numerical data; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D000936:Antigen-Antibody Complex; D000939:Epitopes; D011506:Proteins
keywords: antibody antigen interaction; protein interface prediction; protein–protein interaction