AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models
The study of contact residues and interfacial waters of antibody–antigen (Ab-Ag) structures could help in understanding the principles of antibody–antigen interactions as well as provide guidance for designing antibodies with improved affinities. Given the rapid pace with which new antibody–antigen...
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| Format: | Journal Article |
| Language: | English |
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2019
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| Online Access: | https://hdl.handle.net/10356/106852 http://hdl.handle.net/10220/49677 |
| _version_ | 1826115277471875072 |
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| author | Nguyen, Minh N. Verma, Chandra Shekhar Zhong, Pingyu |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Nguyen, Minh N. Verma, Chandra Shekhar Zhong, Pingyu |
| author_sort | Nguyen, Minh N. |
| collection | NTU |
| description | The study of contact residues and interfacial waters of antibody–antigen (Ab-Ag) structures could help in understanding the principles of antibody–antigen interactions as well as provide guidance for designing antibodies with improved affinities. Given the rapid pace with which new antibody–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–antigen complexes. To the best of our knowledge, this is the first web server for antibody–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–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–antigen interactions and suggest mutations of contact residues to improve affinities of antibodies. |
| first_indexed | 2024-10-01T03:52:52Z |
| format | Journal Article |
| id | ntu-10356/106852 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T03:52:52Z |
| publishDate | 2019 |
| record_format | dspace |
| spelling | ntu-10356/1068522023-02-28T17:06:46Z AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models Nguyen, Minh N. Verma, Chandra Shekhar Zhong, Pingyu School of Biological Sciences Contact Residues Science::Biological sciences Antibody–antigen The study of contact residues and interfacial waters of antibody–antigen (Ab-Ag) structures could help in understanding the principles of antibody–antigen interactions as well as provide guidance for designing antibodies with improved affinities. Given the rapid pace with which new antibody–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–antigen complexes. To the best of our knowledge, this is the first web server for antibody–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–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–antigen interactions and suggest mutations of contact residues to improve affinities of antibodies. NRF (Natl Research Foundation, S’pore) ASTAR (Agency for Sci., Tech. and Research, S’pore) EDB (Economic Devt. Board, S’pore) Published version 2019-08-16T08:47:13Z 2019-12-06T22:19:45Z 2019-08-16T08:47:13Z 2019-12-06T22:19:45Z 2019 Journal Article Nguyen, M. N., Verma, C. S., & Zhong, P. (2019). AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models. Nucleic Acids Research, 47(W1), W482-W489. doi:10.1093/nar/gkz358 0305-1048 https://hdl.handle.net/10356/106852 http://hdl.handle.net/10220/49677 10.1093/nar/gkz358 en Nucleic Acids Research © 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com 8 p. application/pdf |
| spellingShingle | Contact Residues Science::Biological sciences Antibody–antigen Nguyen, Minh N. Verma, Chandra Shekhar Zhong, Pingyu AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models |
| title | AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models |
| title_full | AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models |
| title_fullStr | AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models |
| title_full_unstemmed | AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models |
| title_short | AppA : a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models |
| title_sort | appa a web server for analysis comparison and visualization of contact residues and interfacial waters of antibody antigen structures and models |
| topic | Contact Residues Science::Biological sciences Antibody–antigen |
| url | https://hdl.handle.net/10356/106852 http://hdl.handle.net/10220/49677 |
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