About: Metadynamics in essential coordinates: Free energy simulation of conformational changes

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	We propose an approach that combines an extraction of collective motions of a molecular system with a sampling of its free energy surface. A recently introduced method of metadynamics allows exploration of the free energy surface of a molecular system by means of coarse-grained dynamics with flooding of free energy minima. This free energy surface is defined as a function of a set of collective variables (e.g., interatomic distances, angles, torsions, and others). In this study, essential coordinates determined by essential dynamics (principle component analysis) were used as collective variables in metadynamics. First, dynamics of the model system (explicitly solvated alanine dipeptide, Ace-Ala-Nme) was simulated by a classical molecular dynamics simulation. The trajectory (1 ns) was then analyzed by essential dynamics to obtain essential coordinates. The free energy surface as a function of the first and second essential coordinates was then explored by metadynamics. The resulting free energy surf We propose an approach that combines an extraction of collective motions of a molecular system with a sampling of its free energy surface. A recently introduced method of metadynamics allows exploration of the free energy surface of a molecular system by means of coarse-grained dynamics with flooding of free energy minima. This free energy surface is defined as a function of a set of collective variables (e.g., interatomic distances, angles, torsions, and others). In this study, essential coordinates determined by essential dynamics (principle component analysis) were used as collective variables in metadynamics. First, dynamics of the model system (explicitly solvated alanine dipeptide, Ace-Ala-Nme) was simulated by a classical molecular dynamics simulation. The trajectory (1 ns) was then analyzed by essential dynamics to obtain essential coordinates. The free energy surface as a function of the first and second essential coordinates was then explored by metadynamics. The resulting free energy surf (en) Byla provedena metadynamika v esenciálních soužadnicích (cs)
Title	Metadynamics in essential coordinates: Free energy simulation of conformational changes Metadynamics in essential coordinates: Free energy simulation of conformational changes (en) Metadynamika v esenciálních souřadnicích: modelování volných energií konformačních změn (cs)
skos:prefLabel	Metadynamics in essential coordinates: Free energy simulation of conformational changes Metadynamics in essential coordinates: Free energy simulation of conformational changes (en) Metadynamika v esenciálních souřadnicích: modelování volných energií konformačních změn (cs)
skos:notation	RIV/60461373:22330/07:00019130!RIV08-AV0-22330___
http://linked.open.../vavai/riv/strany	3073-3076
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(KJB500500512), Z(MSM6046137305)
http://linked.open...iv/cisloPeriodika	12
http://linked.open...vai/riv/dodaniDat	2008
http://linked.open...aciTvurceVysledku	Lipovová, Petra Spiwok, Vojtěch Králová, Blanka
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Vysoká škola chemicko-technologická v Praze / Fakulta potravinářské a biochemické technologie
http://linked.open...dnocenehoVysledku	433013
http://linked.open...ai/riv/idVysledku	RIV/60461373:22330/07:00019130
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	metadynamics; free energy surface; essential dynamics (en)
http://linked.open.../riv/klicoveSlovo	metadynamics essential dynamics free energy surface
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[3502DD851D12]
http://linked.open...i/riv/nazevZdroje	JOURNAL OF PHYSICAL CHEMISTRY B
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	3 (xsd:int)
http://linked.open...vavai/riv/projekt	Structural studies of beta-galactosidase from psychrotrophic microorganisms; analysis of biologically and technologically significant complexes
http://linked.open...UplatneniVysledku	2007
http://linked.open...v/svazekPeriodika	111
http://linked.open...iv/tvurceVysledku	Lipovová, Petra Spiwok, Vojtěch Králová, Blanka
http://linked.open...n/vavai/riv/zamer	Teoretické základy potravinářských a biochemických technologií
issn	1520-6106
number of pages	4 (xsd:int)
http://localhost/t...ganizacniJednotka	22330

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