%0 Journal Article
%T AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody每antigen structures and models
%A Chandra S Verma
%A Minh N Nguyen
%A Pingyu Zhong
%J Archive of "Nucleic Acids Research".
%D 2019
%R 10.1093/nar/gkz358
%X The study of contact residues and interfacial waters of antibody每antigen (Ab-Ag) structures could help in understanding the principles of antibody每antigen interactions as well as provide guidance for designing antibodies with improved affinities. Given the rapid pace with which new antibody每antigen structures are deposited in the protein databank (PDB), it is crucial to have computational tools to analyze contact residues and interfacial waters, and investigate them at different levels. In this study, we have developed AppA, a web server that can be used to analyze and compare 3D structures of contact residues and interfacial waters of antibody每antigen complexes. To the best of our knowledge, this is the first web server for antibody每antigen structures equipped with the capability for dissecting the contributions of interfacial water molecules, hydrogen bonds, hydrophobic interactions, van der Waals interactions and ionic interactions at the antibody每antigen interface, and for comparing the structures and conformations of contact residues. Various examples showcase the utility of AppA for such analyses and comparisons that could help in the understanding of antibody每antigen interactions and suggest mutations of contact residues to improve affinities of antibodies. The AppA web server is freely accessible at http://mspc.bii.a-star.edu.sg/minhn/appa.html
%U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602511/