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Development and Application of Computational Methods in Antigen Recognition

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 4445

Special Issue Editors

College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
Interests: AI-driven drug discovery; pharmaceutical biotechnology; pharmacogenomics; neoantigen; computational biology

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Co-Guest Editor
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
Interests: artificial intelligence; neoantigen prediction; precision medicine; bioinformatics; protein design

Special Issue Information

Dear Colleagues,

Antigens recognized by antibodies or T-cell receptors (TCRs) are the key targets of immunotherapy for both cancers and infectious diseases. For example, the design of neoantigen-based vaccines, which has shown a good therapeutic effect in cancer personalized therapy, depends on the accurate identification of tumor neoantigens to a great extent. For infectious diseases, such as COVID-19, the antigenic drift caused by virus mutation is an important factor that reduces the protective effect of vaccine and neutralizing antibodies.

With the development of immunoinformatics and immunogenomics, computational methods such as artificial-intelligence-based methods can play important roles in antigen recognition and vaccine design.

In this Special Issue, we welcome the submission of original research papers, review articles, mini-reviews, and methods papers presenting the development and application of computational methods in antigen recognition. Relevant topics of interest to this Special Issue include (but are not limited to):

  • Recognition of B-cell epitopes;
  • Recognition of T-cell epitopes;
  • Cancer neoantigen prediction;
  • Computational vaccine design;
  • Computational modeling of antigen recognition;
  • Computational modeling of antigen–antibody interaction;
  • Computational modeling of antigen–TCRs interaction.

Dr. Zhan Zhou
Dr. **gCheng Wu
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at mdpi.longhoe.net by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • antigen recognition
  • protein–protein interaction
  • vaccine
  • immune epitope
  • antibody
  • T-cell receptor
  • artificial intelligence

Published Papers (1 paper)

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Research

19 pages, 836 KiB  
Article
Graph Neural Network for Protein–Protein Interaction Prediction: A Comparative Study
by Hang Zhou, Weikun Wang, Jiayun **, Zengwei Zheng and Binbin Zhou
Molecules 2022, 27(18), 6135; https://doi.org/10.3390/molecules27186135 - 19 Sep 2022
Cited by 10 | Viewed by 3971
Abstract
Proteins are the fundamental biological macromolecules which underline practically all biological activities. Protein–protein interactions (PPIs), as they are known, are how proteins interact with other proteins in their environment to perform biological functions. Understanding PPIs reveals how cells behave and operate, such as [...] Read more.
Proteins are the fundamental biological macromolecules which underline practically all biological activities. Protein–protein interactions (PPIs), as they are known, are how proteins interact with other proteins in their environment to perform biological functions. Understanding PPIs reveals how cells behave and operate, such as the antigen recognition and signal transduction in the immune system. In the past decades, many computational methods have been developed to predict PPIs automatically, requiring less time and resources than experimental techniques. In this paper, we present a comparative study of various graph neural networks for protein–protein interaction prediction. Five network models are analyzed and compared, including neural networks (NN), graph convolutional neural networks (GCN), graph attention networks (GAT), hyperbolic neural networks (HNN), and hyperbolic graph convolutions (HGCN). By utilizing the protein sequence information, all of these models can predict the interaction between proteins. Fourteen PPI datasets are extracted and utilized to compare the prediction performance of all these methods. The experimental results show that hyperbolic graph neural networks tend to have a better performance than the other methods on the protein-related datasets. Full article
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