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The Application of Machine Learning for Protein Structure Representation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 4258

Special Issue Editors


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Guest Editor
College of Information Science and Engineering, Hunan University, Changsha 410086, China
Interests: bioinformatics; sequencing data compression; deep learning-based prediction algorithms for disease and drug

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Guest Editor
College of Computer Science and Technology, Jilin University, Changchun 130000, China
Interests: deep learning; computer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, machine learning and deep learning have revolutionized many areas of protein biology with great success. Protein representation is critical in a variety of tasks in biology, such as predicting protein function and structure classification. As the function of a protein is determined by its structure, the structure-based method for determining informative protein representation is a promising solution.

In this Special Issue, we envision that the application of novel machine learning and deep learning algorithms to protein problems will provide practical solutions to improving predictive performance and enhance our understanding protein function. We invite contributions in the form of original research articles presenting sound and innovative methodology.

Dr. Yuansheng Liu
Prof. Dr. Hao Zhang
Guest Editors

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • bioinformatics
  • deep learning
  • protein structure
  • protein function
  • protein–protein interactions
  • protein–peptide interactions
  • compound-protein interactions
  • drug-target interactions

Published Papers (1 paper)

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Research

15 pages, 2557 KiB  
Article
DeepSTABp: A Deep Learning Approach for the Prediction of Thermal Protein Stability
by Felix Jung, Kevin Frey, David Zimmer and Timo Mühlhaus
Int. J. Mol. Sci. 2023, 24(8), 7444; https://doi.org/10.3390/ijms24087444 - 18 Apr 2023
Cited by 9 | Viewed by 3928
Abstract
Proteins are essential macromolecules that carry out a plethora of biological functions. The thermal stability of proteins is an important property that affects their function and determines their suitability for various applications. However, current experimental approaches, primarily thermal proteome profiling, are expensive, labor-intensive, [...] Read more.
Proteins are essential macromolecules that carry out a plethora of biological functions. The thermal stability of proteins is an important property that affects their function and determines their suitability for various applications. However, current experimental approaches, primarily thermal proteome profiling, are expensive, labor-intensive, and have limited proteome and species coverage. To close the gap between available experimental data and sequence information, a novel protein thermal stability predictor called DeepSTABp has been developed. DeepSTABp uses a transformer-based protein language model for sequence embedding and state-of-the-art feature extraction in combination with other deep learning techniques for end-to-end protein melting temperature prediction. DeepSTABp can predict the thermal stability of a wide range of proteins, making it a powerful and efficient tool for large-scale prediction. The model captures the structural and biological properties that impact protein stability, and it allows for the identification of the structural features that contribute to protein stability. DeepSTABp is available to the public via a user-friendly web interface, making it accessible to researchers in various fields. Full article
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