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Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server

Pier Paolo Olimpieri, Anna Chailyan, Anna Tramontano, Paolo Marcatili
2013 Computer applications in the biosciences : CABIOS  
The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts  ...  Results: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen.  ...  ACKNOWLEDGEMENTS The authors are grateful to all other members of the Biocomputing Unit for useful discussions and for testing the server.  ... 
doi:10.1093/bioinformatics/btt369 pmid:23803466 pmcid:PMC3753563 fatcat:khbc2xgm4jc7zdiyldjr6hosju

Ofatumumab Monoclonal Antibody Affinity Maturation Through in silico Modeling

Zahra Payandeh, Masoumeh Rajabibazl, Yousef Mortazavi, Azam Rahimpour, Amir Hossein Taromchi
2017 Iranian Biomedical Journal  
Apoptosis induction is another mechanism of this antibody. Computational docking is the method of predicting the conformation of an antibody-antigen from its separated elements.  ...  Furthermore, the increased antibody affinity can reduce the therapeutic dose of the antibody, resulting in lower toxicity and handling cost.  ...  ACKNOWLEDGMENTS The present study has been financially supported by Research Department of the School of Medicine Shahid Beheshti University of Medical Sciences, Tehran, Iran (grant No. 9571) and Zanjan  ... 
pmid:28992681 pmcid:PMC5889503 fatcat:7pvzljex5ze4dggralvmy3lv3q

Origins of specificity and affinity in antibody–protein interactions

Hung-Pin Peng, Kuo Hao Lee, Jhih-Wei Jian, An-Suei Yang
2014 Proceedings of the National Academy of Sciences of the United States of America  
In developing the efficacy of a therapeutic antibody, optimizing the affinity and specificity of the antibody-antigen interaction mostly relies on selecting and screening from a large pool of random candidates  ...  of the aromatic side chains (9/11) in the antibody-antigen interactions (13).  ...  Peter Kwong (National Institutes of Health) and Dr. Lawrence Shapiro (Columbia University) for helpful discussions.  ... 
doi:10.1073/pnas.1401131111 pmid:24938786 pmcid:PMC4084487 fatcat:wpmmyljakvg2jnyl35fge7xboa

AbAdapt: An adaptive approach to predicting antibody-antigen complex structures from sequence

Ana Davila, Zichang Xu, Songling Li, John Rozewicki, Jan Wilamowski, Sergei Kotelnikov, Dima Kozakov, Shunsuke Teraguchi, Daron M Standley, Michael Gromiha
2022 Bioinformatics Advances  
When epitopes were re-predicted using docking-derived features for specific antibodies, the median ROC AUC increased from 0.679 to 0.720 in cross validation and from 0.694 to 0.730 in the holdout set.  ...  Results To address this need, we have developed AbAdapt, a web server that accepts antibody and antigen sequences, models their 3D structures, predicts epitope and paratope, and then docks the modeled  ...  Acknowledgements We would like to thank all members of the Systems Immunology Lab, the Kozakov Lab, and the late David Ritchie (author of Hex) for very helpful discussions. Funding  ... 
doi:10.1093/bioadv/vbac015 fatcat:wnucz5ovxvbjpb4xuirj46iyde

Progress and challenges in predicting protein interfaces

Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane
2015 Briefings in Bioinformatics  
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.  ...  The most recent method, ISMBLab-PPI, is a neural-network protocol. In contrast to proABC and Antibody i-Patch, its training set is not restrained to antibody-antigen complexes only.  ... 
doi:10.1093/bib/bbv027 pmid:25971595 pmcid:PMC4719070 fatcat:r4rqr4puyvfibktjygqeko5s2e

In silico Techniques for Prospecting and Characterizing Monoclonal Antibodies [chapter]

Tania M. Manieri, Carolina G. Magalhaes, Daniela Y. Takata, João V. Batalha-Carvalho, Ana M. Moro
2020 Monoclonal Antibodies [Working Title]  
In silico methods, such as homology modeling, to predict antibody structures, identification of epitope-paratope interactions, and molecular docking are useful to generate 3D structures of the antibodyantigen  ...  It helps identify the key residues involved in the antigenantibody complex and enable modifications to enhance the antibody binding affinity.  ...  As the improvement of predicting antibody-antigen interaction methods, we expect that the results of paratope prediction, epitope prediction, and antibody-antigen docking methods would offer a valuable  ... 
doi:10.5772/intechopen.94366 fatcat:7tt2sdxmfbcjrkdoobllr6viuu

Biotherapeutics: Challenges and Opportunities for Predictive Toxicology of Monoclonal Antibodies

Dale E Johnson
2018 International Journal of Molecular Sciences  
Mechanisms of toxicity of mAbs are both pharmacological and non-pharmacological in nature; however, standard in silico predictive toxicological methods used in research and development of chemical entities  ...  Challenges and potential opportunities exist for new methodologies to provide a more predictive program to assess and monitor potential adverse drug reactions of mAbs for specific patients before and during  ...  Olimpieri and colleagues [56] developed prediction of Antibody Contacts (proABC), a web server for predicting which residues of an antibody are involved in recognizing its targeted cognate antigen.  ... 
doi:10.3390/ijms19113685 pmid:30469350 fatcat:7ux4wuogvneb7btu2xlu7wuhva

Structural biology in the clouds: The WeNMR-EOSC Ecosystem [article]

Rodrigo Vargas Honorato, Panagiotis I. Koukos, Brian Jiménez-García, Andrei Tsaregorodtsev, Marco Verlato, Andrea Giachetti, Antonio Rosato, Alexandre M.J.J. Bonvin
2021 arXiv   pre-print
Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food  ...  The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.  ...  proABC (Olimpieri et al., 2013) , is a valuable tool that predicts which antibody residues can form intermolecular contacts with its antigen and further give insight into the chemical components of such  ... 
arXiv:2107.01056v1 fatcat:a5v7mp6bxrcg7i7xfo2zonba7y

Methods for sequence and structural analysis of B and T cell receptor repertoires

Shunsuke Teraguchi, Dianita S. Saputri, Mara Anais Llamas-Covarrubias, Ana Davila, Diego Diez, Sedat Aybars Nazlica, John Rozewicki, Hendra S. Ismanto, Jan Wilamowski, Jiaqi Xie, Zichang Xu, Martin de Jesus Loza-Lopez (+3 others)
2020 Computational and Structural Biotechnology Journal  
We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.  ...  The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology.  ...  Acknowledgements We would like to thank all members of the Systems Immunology Lab for helpful discussions.  ... 
doi:10.1016/j.csbj.2020.07.008 pmid:32802272 pmcid:PMC7366105 fatcat:6plaw3q47ffbjli7xzxd2v3se4

Understanding the Significance and Implications of Antibody Numbering and Antigen-Binding Surface/Residue Definition

Mathieu Dondelinger, Patrice Filée, Eric Sauvage, Birgit Quinting, Serge Muyldermans, Moreno Galleni, Marylène S. Vandevenne
2018 Frontiers in Immunology  
chains that affect the binding affinity and/or specificity of the antibody-antigen interaction.  ...  Finally, it discusses the importance of specific sets of residues in the binding affinity and/or specificity of immunoglobulins.  ...  This server identifies ABR by comparing the antibody sequence with a set of antibody-antigen structural complexes (4, 55, 57) .  ... 
doi:10.3389/fimmu.2018.02278 fatcat:haxad3vokjfxjbaukprptfcs6a

Functional and in silico Characterization of Neutralizing Interactions Between Antibodies and the Foot-and-Mouth Disease Virus Immunodominant Antigenic Site

Ruben Marrero Diaz de Villegas, Cristina Seki, Nora M. Mattion, Guido A. König
2021 Frontiers in Veterinary Science  
For foot-and-mouth disease virus (FMDV) research, in particular, computational methods for antigenantibody (Ag–Ab) interaction, and cross-antigenicity characterization and prediction are critical to design  ...  Next, we obtained the variable region sequence of two monoclonal IgM and IgG antibodies that recognize and neutralize antigenic site A (AgSA) epitopes from South America serotype A FMDV and developed two  ...  Julia Sabio y García for their valuable revision of the manuscript.  ... 
doi:10.3389/fvets.2021.554383 pmid:34026880 pmcid:PMC8137985 fatcat:jcxx7fcwmfbmriopl4w5s3ehgu

A Novel Antibody against Human Properdin Inhibits the Alternative Complement System and Specifically Detects Properdin from Blood Samples

Diana Pauly, Benedikt M. Nagel, Jörg Reinders, Tobias Killian, Matthias Wulf, Susanne Ackermann, Boris Ehrenstein, Peter F. Zipfel, Christine Skerka, Bernhard H. F. Weber, Cordula M. Stover
2014 PLoS ONE  
These initial results encourage further investigation into the functional role of properdin in the development, progression and treatment of diseases related to the alternative complement pathway.  ...  Systemic properdin concentrations of healthy controls and patients with age-related macular degeneration or rheumatic diseases were all in the range of 13-30 mg/mL and did not reveal significant differences  ...  Acknowledgments We kindly thank Nicole Schä fer for establishing the hybridoma technology. We are truly grateful to Christopher Dä chert who helped to set up the complement assays.  ... 
doi:10.1371/journal.pone.0096371 pmid:24797388 pmcid:PMC4010523 fatcat:pg6cgk3stjf65cpwgf353jyvxy

Poster

2020 Nippon Saikingaku Zasshi  
To detect specific antigen of H. bilis and H. hepaticus, immunoblot study and identification of the reactive antigen were done.  ...  These results suggest that both administration routes of BLP/antigen complex induce comparable antibody responses.  ...  In four cases, functional MmpL requires the membrane fusion proteinlike protein MmpS. The functional complex of MmpS5/MmpL5 transports anti-mycobacterial drugs including bedaquiline and clofazimine.  ... 
doi:10.3412/jsb.75.60 pmid:31969516 fatcat:jd7bagpexrcyvleh7va5yrohxu