Fine tuning for success in structure-based virtual screening
| العنوان: | Fine tuning for success in structure-based virtual screening |
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| المؤلفون: | Claudia Beato, Emilie Pihan, Obdulia Rabal, Constantino Diaz Gonzalez, Martin Kotev |
| المصدر: | Journal of Computer-Aided Molecular Design. 35:1195-1206 |
| بيانات النشر: | Springer Science and Business Media LLC, 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | Virtual screening, Binding Sites, business.industry, Computer science, Process (engineering), Molecular Conformation, Proteins, Ligands, Supercomputer, computer.software_genre, Automation, Computer Science Applications, Molecular Docking Simulation, Workflow, Docking (molecular), Test set, Drug Discovery, Data mining, Physical and Theoretical Chemistry, business, Protocol (object-oriented programming), computer, Algorithms, Protein Binding |
| الوصف: | Structure-based virtual screening plays a significant role in drug-discovery. The method virtually docks millions of compounds from corporate or public libraries into a binding site of a disease-related protein structure, allowing for the selection of a small list of potential ligands for experimental testing. Many algorithms are available for docking and assessing the affinity of compounds for a targeted protein site. The performance of affinity estimation calculations is highly dependent on the size and nature of the site, therefore a rationale for selecting the best protocol is required. To address this issue, we have developed an automated calibration process, implemented in a Knime workflow. It consists of four steps: preparation of a protein test set with structures and models of the target, preparation of a compound test set with target-related ligands and decoys, automatic test of 24 scoring/rescoring protocols for each target structure and model, and graphical display of results. The automation of the process combined with execution on high performance computing resources greatly reduces the duration of the calibration phase, and the test of many combinations of algorithms on various target conformations results in a rational and optimal choice of the best protocol. Here, we present this tool and exemplify its application in setting-up an optimal protocol for SBVS against Retinoid X Receptor alpha. |
| تدمد: | 1573-4951 0920-654X |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::313050ae92eda0ccaccd52439f831708 https://doi.org/10.1007/s10822-021-00431-4 |
| حقوق: | CLOSED |
| رقم الأكسشن: | edsair.doi.dedup.....313050ae92eda0ccaccd52439f831708 |
| قاعدة البيانات: | OpenAIRE |
Find this article in full text from Springer Verlag. | تدمد: | 15734951 0920654X |
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