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Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery

We here outline the importance of open-source, accessible tools for computer-aided drug discovery (CADD). We begin with a discussion of drug discovery in general to provide context for a subsequent discussion of structure-based CADD applied to small-molecule ligand discovery. Next, we identify usabi...

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Detalles Bibliográficos
Autores principales: Wang, Ann, Durrant, Jacob D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9319651/
https://www.ncbi.nlm.nih.gov/pubmed/35889494
http://dx.doi.org/10.3390/molecules27144623
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author Wang, Ann
Durrant, Jacob D.
author_facet Wang, Ann
Durrant, Jacob D.
author_sort Wang, Ann
collection PubMed
description We here outline the importance of open-source, accessible tools for computer-aided drug discovery (CADD). We begin with a discussion of drug discovery in general to provide context for a subsequent discussion of structure-based CADD applied to small-molecule ligand discovery. Next, we identify usability challenges common to many open-source CADD tools. To address these challenges, we propose a browser-based approach to CADD tool deployment in which CADD calculations run in modern web browsers on users’ local computers. The browser app approach eliminates the need for user-initiated download and installation, ensures broad operating system compatibility, enables easy updates, and provides a user-friendly graphical user interface. Unlike server apps—which run calculations “in the cloud” rather than on users’ local computers—browser apps do not require users to upload proprietary information to a third-party (remote) server. They also eliminate the need for the difficult-to-maintain computer infrastructure required to run user-initiated calculations remotely. We conclude by describing some CADD browser apps developed in our lab, which illustrate the utility of this approach. Aside from introducing readers to these specific tools, we are hopeful that this review highlights the need for additional browser-compatible, user-friendly CADD software.
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spelling pubmed-93196512022-07-27 Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery Wang, Ann Durrant, Jacob D. Molecules Review We here outline the importance of open-source, accessible tools for computer-aided drug discovery (CADD). We begin with a discussion of drug discovery in general to provide context for a subsequent discussion of structure-based CADD applied to small-molecule ligand discovery. Next, we identify usability challenges common to many open-source CADD tools. To address these challenges, we propose a browser-based approach to CADD tool deployment in which CADD calculations run in modern web browsers on users’ local computers. The browser app approach eliminates the need for user-initiated download and installation, ensures broad operating system compatibility, enables easy updates, and provides a user-friendly graphical user interface. Unlike server apps—which run calculations “in the cloud” rather than on users’ local computers—browser apps do not require users to upload proprietary information to a third-party (remote) server. They also eliminate the need for the difficult-to-maintain computer infrastructure required to run user-initiated calculations remotely. We conclude by describing some CADD browser apps developed in our lab, which illustrate the utility of this approach. Aside from introducing readers to these specific tools, we are hopeful that this review highlights the need for additional browser-compatible, user-friendly CADD software. MDPI 2022-07-20 /pmc/articles/PMC9319651/ /pubmed/35889494 http://dx.doi.org/10.3390/molecules27144623 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 Review
Wang, Ann
Durrant, Jacob D.
Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery
title Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery
title_full Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery
title_fullStr Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery
title_full_unstemmed Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery
title_short Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery
title_sort open-source browser-based tools for structure-based computer-aided drug discovery
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9319651/
https://www.ncbi.nlm.nih.gov/pubmed/35889494
http://dx.doi.org/10.3390/molecules27144623
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