Exploring the computational methods for protein-ligand binding site prediction

Computational and Structural Biotechnology Journal
Jingtian ZhaoLe Zhang

Abstract

Proteins participate in various essential processes in vivo via interactions with other molecules. Identifying the residues participating in these interactions not only provides biological insights for protein function studies but also has great significance for drug discoveries. Therefore, predicting protein-ligand binding sites has long been under intense research in the fields of bioinformatics and computer aided drug discovery. In this review, we first introduce the research background of predicting protein-ligand binding sites and then classify the methods into four categories, namely, 3D structure-based, template similarity-based, traditional machine learning-based and deep learning-based methods. We describe representative algorithms in each category and elaborate on machine learning and deep learning-based prediction methods in more detail. Finally, we discuss the trends and challenges of the current research such as molecular dynamics simulation based cryptic binding sites prediction, and highlight prospective directions for the near future.

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Citations

Sep 26, 2020·Expert Opinion on Therapeutic Targets·Gregorio Fernández-BallesterAntonio Ferrer-Montiel
Oct 9, 2020·International Journal of Biological Macromolecules·Nida KhanNavira Qayyum
Apr 10, 2021·Emerging Topics in Life Sciences·Nitu SinghKinshuk Raj Srivastava
Apr 27, 2021·The Journal of Biological Chemistry·Ping-Fang ChenJin Wang
Apr 20, 2021·Journal of Bioinformatics and Computational Biology·Fatemeh NazemAlireza Mehri Dehnavi
May 5, 2021·ChemistryOpen·Joana SmirnovienėDaumantas Matulis
May 12, 2021·The Journal of Physical Chemistry. B·Patrice KoehlHenri Orland
Jun 17, 2021·The Journal of Physical Chemistry. B·Morgan L NanceJeffrey J Gray
Jun 24, 2021·Molecular Diversity·Manish Kumar TripathiPunit Kaur
Jul 24, 2021·Journal of Chemical Information and Modeling·Hugo GuterresWonpil Im
Aug 11, 2021·Journal of Chemical Information and Modeling·Rishal AggarwalU Deva Priyakumar
Oct 27, 2021·Briefings in Bioinformatics·Xuxu WeiHongcai Shang

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Software Mentioned

DBS
SITEHOUND
DTI
FTSite
BLAST
PRED
BindN
DeepConv
LIGSITE
CurPocket

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