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A Review on Parallel Virtual Screening Softwares for High-Performance Computers
Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target asso...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8780228/ https://www.ncbi.nlm.nih.gov/pubmed/35056120 http://dx.doi.org/10.3390/ph15010063 |
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author | Murugan, Natarajan Arul Podobas, Artur Gadioli, Davide Vitali, Emanuele Palermo, Gianluca Markidis, Stefano |
author_facet | Murugan, Natarajan Arul Podobas, Artur Gadioli, Davide Vitali, Emanuele Palermo, Gianluca Markidis, Stefano |
author_sort | Murugan, Natarajan Arul |
collection | PubMed |
description | Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target associated with a disease, and, in addition, they should have favorable pharmacodynamic and pharmacokinetic properties (grouped as ADMET properties). Overall, drug discovery is a multivariable optimization and can be carried out in supercomputers using a reliable scoring function which is a measure of binding affinity or inhibition potential of the drug-like compound. The major problem is that the number of compounds in the chemical spaces is huge, making the computational drug discovery very demanding. However, it is cheaper and less time-consuming when compared to experimental high-throughput screening. As the problem is to find the most stable (global) minima for numerous protein–ligand complexes (on the order of 10 [Formula: see text] to 10 [Formula: see text]), the parallel implementation of in silico virtual screening can be exploited to ensure drug discovery in affordable time. In this review, we discuss such implementations of parallelization algorithms in virtual screening programs. The nature of different scoring functions and search algorithms are discussed, together with a performance analysis of several docking softwares ported on high-performance computing architectures. |
format | Online Article Text |
id | pubmed-8780228 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-87802282022-01-22 A Review on Parallel Virtual Screening Softwares for High-Performance Computers Murugan, Natarajan Arul Podobas, Artur Gadioli, Davide Vitali, Emanuele Palermo, Gianluca Markidis, Stefano Pharmaceuticals (Basel) Article Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target associated with a disease, and, in addition, they should have favorable pharmacodynamic and pharmacokinetic properties (grouped as ADMET properties). Overall, drug discovery is a multivariable optimization and can be carried out in supercomputers using a reliable scoring function which is a measure of binding affinity or inhibition potential of the drug-like compound. The major problem is that the number of compounds in the chemical spaces is huge, making the computational drug discovery very demanding. However, it is cheaper and less time-consuming when compared to experimental high-throughput screening. As the problem is to find the most stable (global) minima for numerous protein–ligand complexes (on the order of 10 [Formula: see text] to 10 [Formula: see text]), the parallel implementation of in silico virtual screening can be exploited to ensure drug discovery in affordable time. In this review, we discuss such implementations of parallelization algorithms in virtual screening programs. The nature of different scoring functions and search algorithms are discussed, together with a performance analysis of several docking softwares ported on high-performance computing architectures. MDPI 2022-01-04 /pmc/articles/PMC8780228/ /pubmed/35056120 http://dx.doi.org/10.3390/ph15010063 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Murugan, Natarajan Arul Podobas, Artur Gadioli, Davide Vitali, Emanuele Palermo, Gianluca Markidis, Stefano A Review on Parallel Virtual Screening Softwares for High-Performance Computers |
title | A Review on Parallel Virtual Screening Softwares for High-Performance Computers |
title_full | A Review on Parallel Virtual Screening Softwares for High-Performance Computers |
title_fullStr | A Review on Parallel Virtual Screening Softwares for High-Performance Computers |
title_full_unstemmed | A Review on Parallel Virtual Screening Softwares for High-Performance Computers |
title_short | A Review on Parallel Virtual Screening Softwares for High-Performance Computers |
title_sort | review on parallel virtual screening softwares for high-performance computers |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8780228/ https://www.ncbi.nlm.nih.gov/pubmed/35056120 http://dx.doi.org/10.3390/ph15010063 |
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