Molecular dynamics studies of proteins
Identifieur interne : 000F81 ( Istex/Corpus ); précédent : 000F80; suivant : 000F82Molecular dynamics studies of proteins
Auteurs : Wilfred F. Van GunsterenSource :
- Current Opinion in Structural Biology [ 0959-440X ] ; 1993.
English descriptors
- KwdEn :
- Teeft :
- Aqueous solution, Basic conditions, Boundary conditions, Computer simulation, Crystal structure, Cytochrome p4socam, Dynamical properties, Dynamics, Electrostatic forces, Ensemble averages, Equilibrium properties, Experimental information, Force field, Free energy, Free energy calculation, Free energy change, Free energy differences, Inhibitor, Inhibitor binding, Initial configuration, Initial structure, Instantaneous restraints, Interatomic interaction function, Molecular, Molecular biophysics, Molecular dynamics, Molecular dynamics simulation, Molecular dynamics simulations, Molecular dynamics studies, Molecular dynamics study, Molecular system, Nato series, Phase space, Photosynthetic reaction center, Protein, Protein mutants, Protein structure, Relative stability, Sampling periods, Simulation, Simulation techniques, Spatial structure, Structural stability, Such simulations, Water molecules, White lysozyme.
Abstract
Molecular dynamics computer simulation studies of proteins are considered. Standard applications are the calculation of equilibrium properties, binding constants and the use of molecular dynamics simulation in the refinement of protein structure based on NMR or X-ray diffraction data. In addition, simulation of non-equilibrium processes and methodological studies are briefly discussed. Computer simulation is a very useful explorative tool with which to investigate protein structure, dynamics and function, provided it is used with a clear eye to its strengths and limitations.
Url:
DOI: 10.1016/S0959-440X(05)80164-2
Links to Exploration step
ISTEX:FBC836CC6C1F673CFC1C196785D7488E4840DF99Le document en format XML
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Van Gunsteren</name><affiliation><mods:affiliation>Physical Chemistry, ETH-Zentrum, CH-8092, Zurich, Switzerland</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:FBC836CC6C1F673CFC1C196785D7488E4840DF99</idno><date when="1993" year="1993">1993</date><idno type="doi">10.1016/S0959-440X(05)80164-2</idno><idno type="url">https://api.istex.fr/ark:/67375/6H6-KJHZW5L3-6/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">000F81</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000F81</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Molecular dynamics studies of proteins</title><author><name sortKey="Van Gunsteren, Wilfred F" sort="Van Gunsteren, Wilfred F" uniqKey="Van Gunsteren W" first="Wilfred F." last="Van Gunsteren">Wilfred F. Van Gunsteren</name><affiliation><mods:affiliation>Physical Chemistry, ETH-Zentrum, CH-8092, Zurich, Switzerland</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Current Opinion in Structural Biology</title><title level="j" type="abbrev">COSTBI</title><idno type="ISSN">0959-440X</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1993">1993</date><biblScope unit="volume">3</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="277">277</biblScope><biblScope unit="page" to="281">281</biblScope></imprint><idno type="ISSN">0959-440X</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0959-440X</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>BPTI</term><term>MD</term><term>NOE</term></keywords><keywords scheme="Teeft" xml:lang="en"><term>Aqueous solution</term><term>Basic conditions</term><term>Boundary conditions</term><term>Computer simulation</term><term>Crystal structure</term><term>Cytochrome p4socam</term><term>Dynamical properties</term><term>Dynamics</term><term>Electrostatic forces</term><term>Ensemble averages</term><term>Equilibrium properties</term><term>Experimental information</term><term>Force field</term><term>Free energy</term><term>Free energy calculation</term><term>Free energy change</term><term>Free energy differences</term><term>Inhibitor</term><term>Inhibitor binding</term><term>Initial configuration</term><term>Initial structure</term><term>Instantaneous restraints</term><term>Interatomic interaction function</term><term>Molecular</term><term>Molecular biophysics</term><term>Molecular dynamics</term><term>Molecular dynamics simulation</term><term>Molecular dynamics simulations</term><term>Molecular dynamics studies</term><term>Molecular dynamics study</term><term>Molecular system</term><term>Nato series</term><term>Phase space</term><term>Photosynthetic reaction center</term><term>Protein</term><term>Protein mutants</term><term>Protein structure</term><term>Relative stability</term><term>Sampling periods</term><term>Simulation</term><term>Simulation techniques</term><term>Spatial structure</term><term>Structural stability</term><term>Such simulations</term><term>Water molecules</term><term>White lysozyme</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Molecular dynamics computer simulation studies of proteins are considered. Standard applications are the calculation of equilibrium properties, binding constants and the use of molecular dynamics simulation in the refinement of protein structure based on NMR or X-ray diffraction data. In addition, simulation of non-equilibrium processes and methodological studies are briefly discussed. Computer simulation is a very useful explorative tool with which to investigate protein structure, dynamics and function, provided it is used with a clear eye to its strengths and limitations.</div></front></TEI><istex><corpusName>elsevier</corpusName><keywords><teeft><json:string>simulation</json:string><json:string>computer simulation</json:string><json:string>molecular system</json:string><json:string>molecular dynamics</json:string><json:string>molecular dynamics simulation</json:string><json:string>dynamics</json:string><json:string>water molecules</json:string><json:string>protein structure</json:string><json:string>molecular dynamics simulations</json:string><json:string>photosynthetic reaction center</json:string><json:string>relative stability</json:string><json:string>basic conditions</json:string><json:string>ensemble averages</json:string><json:string>cytochrome p4socam</json:string><json:string>inhibitor</json:string><json:string>free energy calculation</json:string><json:string>boundary conditions</json:string><json:string>dynamical properties</json:string><json:string>equilibrium properties</json:string><json:string>spatial structure</json:string><json:string>protein mutants</json:string><json:string>simulation techniques</json:string><json:string>molecular biophysics</json:string><json:string>molecular dynamics study</json:string><json:string>nato series</json:string><json:string>free energy</json:string><json:string>initial configuration</json:string><json:string>sampling periods</json:string><json:string>free energy differences</json:string><json:string>free energy change</json:string><json:string>phase space</json:string><json:string>initial structure</json:string><json:string>aqueous solution</json:string><json:string>crystal structure</json:string><json:string>white lysozyme</json:string><json:string>experimental information</json:string><json:string>such simulations</json:string><json:string>instantaneous restraints</json:string><json:string>electrostatic forces</json:string><json:string>structural stability</json:string><json:string>molecular dynamics studies</json:string><json:string>interatomic interaction function</json:string><json:string>inhibitor binding</json:string><json:string>force field</json:string><json:string>molecular</json:string><json:string>protein</json:string></teeft></keywords><author><json:item><name>Wilfred F. van Gunsteren</name><affiliations><json:string>Physical Chemistry, ETH-Zentrum, CH-8092, Zurich, Switzerland</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Theory and simulation</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>BPTI : bovine pancreatic trypsin inhibitor</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MD : molecular dynamics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>NOE : nuclear Overhauser effect</value></json:item></subject><articleId><json:string>05801642</json:string></articleId><arkIstex>ark:/67375/6H6-KJHZW5L3-6</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>Full-length article</json:string></originalGenre><abstract>Molecular dynamics computer simulation studies of proteins are considered. Standard applications are the calculation of equilibrium properties, binding constants and the use of molecular dynamics simulation in the refinement of protein structure based on NMR or X-ray diffraction data. In addition, simulation of non-equilibrium processes and methodological studies are briefly discussed. Computer simulation is a very useful explorative tool with which to investigate protein structure, dynamics and function, provided it is used with a clear eye to its strengths and limitations.</abstract><qualityIndicators><score>5.819</score><pdfWordCount>2847</pdfWordCount><pdfCharCount>21989</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>5</pdfPageCount><pdfPageSize>611.84 x 791.84 pts</pdfPageSize><refBibsNative>true</refBibsNative><abstractWordCount>81</abstractWordCount><abstractCharCount>581</abstractCharCount><keywordCount>4</keywordCount></qualityIndicators><title>Molecular dynamics studies of proteins</title><pii><json:string>S0959-440X(05)80164-2</json:string></pii><genre><json:string>research-article</json:string></genre><host><title>Current Opinion in Structural Biology</title><language><json:string>unknown</json:string></language><publicationDate>1993</publicationDate><issn><json:string>0959-440X</json:string></issn><pii><json:string>S0959-440X(05)X0147-6</json:string></pii><volume>3</volume><issue>2</issue><pages><first>277</first><last>281</last></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>1993</json:string></date><geogName></geogName><orgName></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Guenot</json:string><json:string>In</json:string><json:string>Kollman</json:string></persName><placeName></placeName><ref_url></ref_url><ref_bibl><json:string>[18]</json:string><json:string>[45-47]</json:string><json:string>[44]</json:string><json:string>[8]</json:string><json:string>Lounnas et al. [51]</json:string><json:string>Bala et al.</json:string><json:string>[43]</json:string><json:string>[30,31]</json:string><json:string>[49]</json:string><json:string>[3]</json:string><json:string>[53]</json:string><json:string>Cummins et al</json:string><json:string>[48]</json:string><json:string>[52]</json:string><json:string>[28,29]</json:string><json:string>[36]</json:string><json:string>[4-6]</json:string><json:string>[24]</json:string><json:string>[19]</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/6H6-KJHZW5L3-6</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - cell biology</json:string><json:string>2 - biochemistry & molecular biology</json:string></wos><scienceMetrix><json:string>1 - health sciences</json:string><json:string>2 - biomedical research</json:string><json:string>3 - biophysics</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Molecular Biology</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Structural Biology</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string></inist></categories><publicationDate>1993</publicationDate><copyrightDate>1993</copyrightDate><doi><json:string>10.1016/S0959-440X(05)80164-2</json:string></doi><id>FBC836CC6C1F673CFC1C196785D7488E4840DF99</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-KJHZW5L3-6/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-KJHZW5L3-6/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/6H6-KJHZW5L3-6/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main" xml:lang="en">Molecular dynamics studies of proteins</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher scheme="https://scientific-publisher.data.istex.fr">ELSEVIER</publisher><availability><licence><p>©1993 Current Biology Ltd</p></licence><p scheme="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</p></availability><date>1993</date></publicationStmt><notesStmt><note type="research-article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</note><note type="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Molecular dynamics studies of proteins</title><author xml:id="author-0000"><persName><forename type="first">Wilfred F.</forename><surname>van Gunsteren</surname></persName><affiliation>Physical Chemistry, ETH-Zentrum, CH-8092, Zurich, Switzerland</affiliation></author><idno type="istex">FBC836CC6C1F673CFC1C196785D7488E4840DF99</idno><idno type="ark">ark:/67375/6H6-KJHZW5L3-6</idno><idno type="DOI">10.1016/S0959-440X(05)80164-2</idno><idno type="PII">S0959-440X(05)80164-2</idno><idno type="article-id">05801642</idno></analytic><monogr><title level="j">Current Opinion in Structural Biology</title><title level="j" type="abbrev">COSTBI</title><idno type="pISSN">0959-440X</idno><idno type="PII">S0959-440X(05)X0147-6</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1993"></date><biblScope unit="volume">3</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="277">277</biblScope><biblScope unit="page" to="281">281</biblScope></imprint></monogr></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>1993</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Molecular dynamics computer simulation studies of proteins are considered. Standard applications are the calculation of equilibrium properties, binding constants and the use of molecular dynamics simulation in the refinement of protein structure based on NMR or X-ray diffraction data. In addition, simulation of non-equilibrium processes and methodological studies are briefly discussed. Computer simulation is a very useful explorative tool with which to investigate protein structure, dynamics and function, provided it is used with a clear eye to its strengths and limitations.</p></abstract><textClass><keywords scheme="keyword"><list><head>article-category</head><item><term>Theory and simulation</term></item></list></keywords></textClass><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Abbreviations</head><item><term>BPTI</term><term>bovine pancreatic trypsin inhibitor</term></item><item><term>MD</term><term>molecular dynamics</term></item><item><term>NOE</term><term>nuclear Overhauser effect</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="1993">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-KJHZW5L3-6/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Elsevier doc found" wicri:toSee="Elsevier, no converted or simple article"><istex:xmlDeclaration>version="1.0" encoding="utf-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//ES//DTD journal article DTD version 5.0.1//EN//XML" URI="art501.dtd" name="istex:docType"></istex:docType><istex:document><article version="5.0" xml:lang="en" docsubtype="fla"><item-info><jid>COSTBI</jid><aid>05801642</aid><ce:pii>S0959-440X(05)80164-2</ce:pii><ce:doi>10.1016/S0959-440X(05)80164-2</ce:doi><ce:copyright type="unknown" year="1993">Current Biology Ltd</ce:copyright><ce:doctopics><ce:doctopic><ce:text>Theory and simulation</ce:text></ce:doctopic></ce:doctopics></item-info><head><ce:title>Molecular dynamics studies of proteins</ce:title><ce:author-group><ce:author><ce:given-name>Wilfred F.</ce:given-name><ce:surname>van Gunsteren</ce:surname></ce:author><ce:affiliation id="aff1"><ce:textfn>Physical Chemistry, ETH-Zentrum, CH-8092, Zurich, Switzerland</ce:textfn></ce:affiliation></ce:author-group><ce:abstract id="ab1" class="author" xml:lang="en"><ce:abstract-sec><ce:simple-para>Molecular dynamics computer simulation studies of proteins are considered. Standard applications are the calculation of equilibrium properties, binding constants and the use of molecular dynamics simulation in the refinement of protein structure based on NMR or X-ray diffraction data. In addition, simulation of non-equilibrium processes and methodological studies are briefly discussed. Computer simulation is a very useful explorative tool with which to investigate protein structure, dynamics and function, provided it is used with a clear eye to its strengths and limitations.</ce:simple-para></ce:abstract-sec></ce:abstract><ce:keywords class="abr" xml:lang="en"><ce:section-title>Abbreviations</ce:section-title><ce:keyword><ce:text>BPTI</ce:text><ce:keyword><ce:text>bovine pancreatic trypsin inhibitor</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>MD</ce:text><ce:keyword><ce:text>molecular dynamics</ce:text></ce:keyword></ce:keyword><ce:keyword><ce:text>NOE</ce:text><ce:keyword><ce:text>nuclear Overhauser effect</ce:text></ce:keyword></ce:keyword></ce:keywords></head><tail><ce:bibliography><ce:section-title>References and recommended reading</ce:section-title><ce:bibliography-sec><ce:bib-reference id="bib1"><ce:label>1.</ce:label><sb:reference><sb:contribution langtype="en"><sb:authors><sb:author><ce:surname>van Gunsteren</ce:surname><ce:given-name>WF</ce:given-name></sb:author><sb:author><ce:surname>Mark</ce:surname><ce:given-name>AE</ce:given-name></sb:author></sb:authors><sb:title><sb:maintitle>On the Interpretation of Bio-chemical Data by Molecular Dynamics Computer Simulation</sb:maintitle></sb:title></sb:contribution><sb:host><sb:issue><sb:series><sb:title><sb:maintitle>Eur J Biochem</sb:maintitle></sb:title><sb:volume-nr>204</sb:volume-nr></sb:series><sb:date>1992</sb:date></sb:issue><sb:pages><sb:first-page>947</sb:first-page><sb:last-page>961</sb:last-page></sb:pages></sb:host></sb:reference></ce:bib-reference><ce:bib-reference id="bib2"><ce:label>••</ce:label><ce:note><ce:simple-para>Papers of particular interest, published within the annual period of review, have been highlighted as: of outstanding interest</ce:simple-para></ce:note></ce:bib-reference></ce:bibliography-sec></ce:bibliography></tail></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Molecular dynamics studies of proteins</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>Molecular dynamics studies of proteins</title></titleInfo><name type="personal"><namePart type="given">Wilfred F.</namePart><namePart type="family">van Gunsteren</namePart><affiliation>Physical Chemistry, ETH-Zentrum, CH-8092, Zurich, Switzerland</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="Full-length article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1993</dateIssued><copyrightDate encoding="w3cdtf">1993</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><abstract lang="en">Molecular dynamics computer simulation studies of proteins are considered. Standard applications are the calculation of equilibrium properties, binding constants and the use of molecular dynamics simulation in the refinement of protein structure based on NMR or X-ray diffraction data. In addition, simulation of non-equilibrium processes and methodological studies are briefly discussed. Computer simulation is a very useful explorative tool with which to investigate protein structure, dynamics and function, provided it is used with a clear eye to its strengths and limitations.</abstract><subject><genre>article-category</genre><topic>Theory and simulation</topic></subject><subject lang="en"><genre>Abbreviations</genre><topic>BPTI : bovine pancreatic trypsin inhibitor</topic><topic>MD : molecular dynamics</topic><topic>NOE : nuclear Overhauser effect</topic></subject><relatedItem type="host"><titleInfo><title>Current Opinion in Structural Biology</title></titleInfo><titleInfo type="abbreviated"><title>COSTBI</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>ELSEVIER</publisher><dateIssued encoding="w3cdtf">1993</dateIssued></originInfo><identifier type="ISSN">0959-440X</identifier><identifier type="PII">S0959-440X(05)X0147-6</identifier><part><date>1993</date><detail type="volume"><number>3</number><caption>vol.</caption></detail><detail type="issue"><number>2</number><caption>no.</caption></detail><extent unit="issue-pages"><start>165</start><end>310</end></extent><extent unit="pages"><start>277</start><end>281</end></extent></part></relatedItem><identifier type="istex">FBC836CC6C1F673CFC1C196785D7488E4840DF99</identifier><identifier type="ark">ark:/67375/6H6-KJHZW5L3-6</identifier><identifier type="DOI">10.1016/S0959-440X(05)80164-2</identifier><identifier type="PII">S0959-440X(05)80164-2</identifier><identifier type="ArticleID">05801642</identifier><accessCondition type="use and reproduction" contentType="copyright">©1993 Current Biology Ltd</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-HKKZVM7B-M">elsevier</recordContentSource><recordOrigin>Current Biology Ltd, ©1993</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/6H6-KJHZW5L3-6/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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