Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, David Bednar
{"title":"pyCaverDock: Python实现的流行工具，用于分析配体传输，具有高级缓存和批处理计算支持。","authors":"Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, David Bednar","doi":"10.1093/bioinformatics/btad443","DOIUrl":null,"url":null,"abstract":"<p><strong>Summary: </strong>Access pathways in enzymes are crucial for the passage of substrates and products of catalysed reactions. The process can be studied by computational means with variable degrees of precision. Our in-house approximative method CaverDock provides a fast and easy way to set up and run ligand binding and unbinding calculations through protein tunnels and channels. Here we introduce pyCaverDock, a Python3 API designed to improve user experience with the tool and further facilitate the ligand transport analyses. The API enables users to simplify the steps needed to use CaverDock, from automatizing setup processes to designing screening pipelines.</p><p><strong>Availability and implementation: </strong>pyCaverDock API is implemented in Python 3 and is freely available with detailed documentation and practical examples at https://loschmidt.chemi.muni.cz/caverdock/.</p>","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"39 8","pages":""},"PeriodicalIF":4.4000,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10397418/pdf/","citationCount":"0","resultStr":"{\"title\":\"pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support.\",\"authors\":\"Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, David Bednar\",\"doi\":\"10.1093/bioinformatics/btad443\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Summary: </strong>Access pathways in enzymes are crucial for the passage of substrates and products of catalysed reactions. The process can be studied by computational means with variable degrees of precision. Our in-house approximative method CaverDock provides a fast and easy way to set up and run ligand binding and unbinding calculations through protein tunnels and channels. Here we introduce pyCaverDock, a Python3 API designed to improve user experience with the tool and further facilitate the ligand transport analyses. The API enables users to simplify the steps needed to use CaverDock, from automatizing setup processes to designing screening pipelines.</p><p><strong>Availability and implementation: </strong>pyCaverDock API is implemented in Python 3 and is freely available with detailed documentation and practical examples at https://loschmidt.chemi.muni.cz/caverdock/.</p>\",\"PeriodicalId\":8903,\"journal\":{\"name\":\"Bioinformatics\",\"volume\":\"39 8\",\"pages\":\"\"},\"PeriodicalIF\":4.4000,\"publicationDate\":\"2023-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10397418/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/bioinformatics/btad443\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/bioinformatics/btad443","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support.
Summary: Access pathways in enzymes are crucial for the passage of substrates and products of catalysed reactions. The process can be studied by computational means with variable degrees of precision. Our in-house approximative method CaverDock provides a fast and easy way to set up and run ligand binding and unbinding calculations through protein tunnels and channels. Here we introduce pyCaverDock, a Python3 API designed to improve user experience with the tool and further facilitate the ligand transport analyses. The API enables users to simplify the steps needed to use CaverDock, from automatizing setup processes to designing screening pipelines.
Availability and implementation: pyCaverDock API is implemented in Python 3 and is freely available with detailed documentation and practical examples at https://loschmidt.chemi.muni.cz/caverdock/.
期刊介绍：
The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.
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