Application of the molecular dynamics simulation GROMACS in food science
[Display omitted] •The GROMACS molecular dynamics simulation software for food research is summarized.•The advantages and procedure of GROMACS for food research are summarized.•GROMACS provides valuable guidance for studying the properties of food molecules.•GROMACS can be used in food processing an...
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Veröffentlicht in: | Food research international 2024-08, Vol.190, p.114653, Article 114653 |
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container_title | Food research international |
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creator | Yu, Dongping Li, Haiping Liu, Yuzi Yang, Xingqun Yang, Wei Fu, Yiran Zuo, Yi-ao Huang, Xianya |
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•The GROMACS molecular dynamics simulation software for food research is summarized.•The advantages and procedure of GROMACS for food research are summarized.•GROMACS provides valuable guidance for studying the properties of food molecules.•GROMACS can be used in food processing and food interaction.
Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food. |
doi_str_mv | 10.1016/j.foodres.2024.114653 |
format | Article |
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•The GROMACS molecular dynamics simulation software for food research is summarized.•The advantages and procedure of GROMACS for food research are summarized.•GROMACS provides valuable guidance for studying the properties of food molecules.•GROMACS can be used in food processing and food interaction.
Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.</description><identifier>ISSN: 0963-9969</identifier><identifier>ISSN: 1873-7145</identifier><identifier>EISSN: 1873-7145</identifier><identifier>DOI: 10.1016/j.foodres.2024.114653</identifier><identifier>PMID: 38945587</identifier><language>eng</language><publisher>Canada: Elsevier Ltd</publisher><subject>computer simulation ; computer software ; Food components ; food research ; Food science ; Food Technology - methods ; GROMACS ; molecular dynamics ; Molecular Dynamics Simulation ; Molecular interaction ; Software</subject><ispartof>Food research international, 2024-08, Vol.190, p.114653, Article 114653</ispartof><rights>2024 Elsevier Ltd</rights><rights>Copyright © 2024 Elsevier Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c346t-35afc9f118f1708f6a9ece2ea3b8433efeb0291b3310759874f5f39336268f723</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0963996924007233$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38945587$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yu, Dongping</creatorcontrib><creatorcontrib>Li, Haiping</creatorcontrib><creatorcontrib>Liu, Yuzi</creatorcontrib><creatorcontrib>Yang, Xingqun</creatorcontrib><creatorcontrib>Yang, Wei</creatorcontrib><creatorcontrib>Fu, Yiran</creatorcontrib><creatorcontrib>Zuo, Yi-ao</creatorcontrib><creatorcontrib>Huang, Xianya</creatorcontrib><title>Application of the molecular dynamics simulation GROMACS in food science</title><title>Food research international</title><addtitle>Food Res Int</addtitle><description>[Display omitted]
•The GROMACS molecular dynamics simulation software for food research is summarized.•The advantages and procedure of GROMACS for food research are summarized.•GROMACS provides valuable guidance for studying the properties of food molecules.•GROMACS can be used in food processing and food interaction.
Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.</description><subject>computer simulation</subject><subject>computer software</subject><subject>Food components</subject><subject>food research</subject><subject>Food science</subject><subject>Food Technology - methods</subject><subject>GROMACS</subject><subject>molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecular interaction</subject><subject>Software</subject><issn>0963-9969</issn><issn>1873-7145</issn><issn>1873-7145</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkE1rGzEQhkVJady0PyFhj7msq9nRx-pUjEmdQkqgH2cha0dUZnflSOtC_n3XtdNrTgPD8847PIxdA18CB_VptwwpdZnKsuGNWAIIJfENW0CrsdYg5AVbcKOwNkaZS_a-lB3nXElt3rFLbI2QstULdr_a7_vo3RTTWKVQTb-pGlJP_tC7XHXPoxuiL1WJw7z4B22-P35brX9UcayOH1TFRxo9fWBvg-sLfTzPK_bry93P9X398Lj5ul491B6FmmqULngTANoAmrdBOUOeGnK4bQUiBdryxsAWEbiWptUiyIAGUTWqDbrBK3Z7urvP6elAZbJDLJ763o2UDsUiSFRCAPDXUa4FzEVwvCpPqM-plEzB7nMcXH62wO3Rt93Zs2979G1PvufczbnisB2o-596ETwDn08AzU7-RMr27KuLmfxkuxRfqfgL-_KSGw</recordid><startdate>202408</startdate><enddate>202408</enddate><creator>Yu, Dongping</creator><creator>Li, Haiping</creator><creator>Liu, Yuzi</creator><creator>Yang, Xingqun</creator><creator>Yang, Wei</creator><creator>Fu, Yiran</creator><creator>Zuo, Yi-ao</creator><creator>Huang, Xianya</creator><general>Elsevier Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope></search><sort><creationdate>202408</creationdate><title>Application of the molecular dynamics simulation GROMACS in food science</title><author>Yu, Dongping ; Li, Haiping ; Liu, Yuzi ; Yang, Xingqun ; Yang, Wei ; Fu, Yiran ; Zuo, Yi-ao ; Huang, Xianya</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c346t-35afc9f118f1708f6a9ece2ea3b8433efeb0291b3310759874f5f39336268f723</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>computer simulation</topic><topic>computer software</topic><topic>Food components</topic><topic>food research</topic><topic>Food science</topic><topic>Food Technology - methods</topic><topic>GROMACS</topic><topic>molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>Molecular interaction</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yu, Dongping</creatorcontrib><creatorcontrib>Li, Haiping</creatorcontrib><creatorcontrib>Liu, Yuzi</creatorcontrib><creatorcontrib>Yang, Xingqun</creatorcontrib><creatorcontrib>Yang, Wei</creatorcontrib><creatorcontrib>Fu, Yiran</creatorcontrib><creatorcontrib>Zuo, Yi-ao</creatorcontrib><creatorcontrib>Huang, Xianya</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Food research international</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yu, Dongping</au><au>Li, Haiping</au><au>Liu, Yuzi</au><au>Yang, Xingqun</au><au>Yang, Wei</au><au>Fu, Yiran</au><au>Zuo, Yi-ao</au><au>Huang, Xianya</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Application of the molecular dynamics simulation GROMACS in food science</atitle><jtitle>Food research international</jtitle><addtitle>Food Res Int</addtitle><date>2024-08</date><risdate>2024</risdate><volume>190</volume><spage>114653</spage><pages>114653-</pages><artnum>114653</artnum><issn>0963-9969</issn><issn>1873-7145</issn><eissn>1873-7145</eissn><abstract>[Display omitted]
•The GROMACS molecular dynamics simulation software for food research is summarized.•The advantages and procedure of GROMACS for food research are summarized.•GROMACS provides valuable guidance for studying the properties of food molecules.•GROMACS can be used in food processing and food interaction.
Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.</abstract><cop>Canada</cop><pub>Elsevier Ltd</pub><pmid>38945587</pmid><doi>10.1016/j.foodres.2024.114653</doi></addata></record> |
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subjects | computer simulation computer software Food components food research Food science Food Technology - methods GROMACS molecular dynamics Molecular Dynamics Simulation Molecular interaction Software |
title | Application of the molecular dynamics simulation GROMACS in food science |
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