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Given the rapid pace with which new antibody\u2013antigen 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\u2013antigen complexes. To the best of our knowledge, this is the first web server for antibody\u2013antigen 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\u2013antigen 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\u2013antigen 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.<\/jats:p>","DOI":"10.1093\/nar\/gkz358","type":"journal-article","created":{"date-parts":[[2019,4,27]],"date-time":"2019-04-27T02:32:39Z","timestamp":1556332359000},"page":"W482-W489","source":"Crossref","is-referenced-by-count":9,"title":["AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody\u2013antigen structures and models"],"prefix":"10.1093","volume":"47","author":[{"given":"Minh N","family":"Nguyen","sequence":"first","affiliation":[{"name":"Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671"}]},{"given":"Chandra S","family":"Verma","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671"},{"name":"Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543"},{"name":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551"}]},{"given":"Pingyu","family":"Zhong","sequence":"additional","affiliation":[{"name":"Singapore Immunology Network (SIgN), 8A Biomedical Grove, Immunos Building, Level 4, Singapore 138648"}]}],"member":"286","published-online":{"date-parts":[[2019,5,9]]},"reference":[{"key":"2019062808131279200_B1","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1093\/bioinformatics\/btt369","article-title":"Prediction of site-specific interactions in antibody\u2013antigen complexes: the proABC method and server","volume":"29","author":"Olimpieri","year":"2013","journal-title":"Bioinformatics"},{"key":"2019062808131279200_B2","doi-asserted-by":"crossref","first-page":"E2656","DOI":"10.1073\/pnas.1401131111","article-title":"Origins of specificity and affinity in antibody-protein interactions","volume":"111","author":"Peng","year":"2014","journal-title":"Proc. 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