Literature DB >> 35911958

Antibody-Antigen Binding Interface Analysis in the Big Data Era.

Pedro B P S Reis1,2, German P Barletta1,3,4, Luca Gagliardi1, Sara Fortuna1, Miguel A Soler1,5, Walter Rocchia1.   

Abstract

Antibodies have become the Swiss Army tool for molecular biology and nanotechnology. Their outstanding ability to specifically recognise molecular antigens allows their use in many different applications from medicine to the industry. Moreover, the improvement of conventional structural biology techniques (e.g., X-ray, NMR) as well as the emergence of new ones (e.g., Cryo-EM), have permitted in the last years a notable increase of resolved antibody-antigen structures. This offers a unique opportunity to perform an exhaustive structural analysis of antibody-antigen interfaces by employing the large amount of data available nowadays. To leverage this factor, different geometric as well as chemical descriptors were evaluated to perform a comprehensive characterization.
Copyright © 2022 Reis, Barletta, Gagliardi, Fortuna, Soler and Rocchia.

Entities:  

Keywords:  antibody-antigen complex; complementarity-determining region (CDR); epitope analysis; paratope analysis; structure analysis and characterization

Year:  2022        PMID: 35911958      PMCID: PMC9329859          DOI: 10.3389/fmolb.2022.945808

Source DB:  PubMed          Journal:  Front Mol Biosci        ISSN: 2296-889X


  34 in total

1.  Origins of specificity and affinity in antibody-protein interactions.

Authors:  Hung-Pin Peng; Kuo Hao Lee; Jhih-Wei Jian; An-Suei Yang
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-17       Impact factor: 11.205

Review 2.  The Increasingly Human and Profitable Monoclonal Antibody Market.

Authors:  António L Grilo; A Mantalaris
Journal:  Trends Biotechnol       Date:  2018-06-23       Impact factor: 19.536

3.  Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking.

Authors:  Daisuke Kuroda; Jeffrey J Gray
Journal:  Bioinformatics       Date:  2016-04-19       Impact factor: 6.937

4.  Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures.

Authors:  Thiruvarangan Ramaraj; Thomas Angel; Edward A Dratz; Algirdas J Jesaitis; Brendan Mumey
Journal:  Biochim Biophys Acta       Date:  2012-01-10

5.  PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations.

Authors:  Pedro B P S Reis; Diogo Vila-Viçosa; Walter Rocchia; Miguel Machuqueiro
Journal:  J Chem Inf Model       Date:  2020-09-16       Impact factor: 4.956

6.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505

7.  Correlation between segmental mobility and the location of antigenic determinants in proteins.

Authors:  E Westhof; D Altschuh; D Moras; A C Bloomer; A Mondragon; A Klug; M H Van Regenmortel
Journal:  Nature       Date:  1984 Sep 13-19       Impact factor: 49.962

8.  Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution.

Authors:  Sergio Decherchi; José Colmenares; Chiara Eva Catalano; Michela Spagnuolo; Emil Alexov; Walter Rocchia
Journal:  Commun Comput Phys       Date:  2012-12-06       Impact factor: 3.246

Review 9.  Neutralizing monoclonal antibodies for treatment of COVID-19.

Authors:  Peter C Taylor; Andrew C Adams; Matthew M Hufford; Inmaculada de la Torre; Kevin Winthrop; Robert L Gottlieb
Journal:  Nat Rev Immunol       Date:  2021-04-19       Impact factor: 108.555

Review 10.  Emerging new therapeutic antibody derivatives for cancer treatment.

Authors:  Shijie Jin; Yanping Sun; Xiao Liang; Xinyu Gu; Jiangtao Ning; Yingchun Xu; Shuqing Chen; Liqiang Pan
Journal:  Signal Transduct Target Ther       Date:  2022-02-07
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