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Current Protein & Peptide Science

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ISSN (Print): 1389-2037
ISSN (Online): 1875-5550

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Review Article

Current Stage and Future Perspectives for Homology Modeling, Molecular Dynamics Simulations, Machine Learning with Molecular Dynamics, and Quantum Computing for Intrinsically Disordered Proteins and Proteins with Intrinsically Disordered Regions

Author(s): Orkid Coskuner-Weber* and Vladimir N. Uversky

Volume 25, Issue 2, 2024

Published on: 02 January, 2024

Page: [163 - 171] Pages: 9

DOI: 10.2174/0113892037281184231123111223

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Abstract

The structural ensembles of intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) cannot be easily characterized using conventional experimental techniques. Computational techniques complement experiments and provide useful insights into the structural ensembles of IDPs and proteins with IDRs. Herein, we discuss computational techniques such as homology modeling, molecular dynamics simulations, machine learning with molecular dynamics, and quantum computing that can be applied to the studies of IDPs and hybrid proteins with IDRs. We also provide useful future perspectives for computational techniques that can be applied to IDPs and hybrid proteins containing ordered domains and IDRs.

Keywords: Homology modeling, molecular dynamics simulations, machine learning with molecular dynamics, quantum computing, intrinsically disordered proteins, proteins with intrinsically disordered regions.

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