About: A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects Goto Sponge NotDistinct Permalink

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

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	A procedure for deriving force field torsion parameters including certain previously neglected solvation effects is suggested. In contrast to the conventional in vacuo approaches, the dihedral parameters are obtained from the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. An analysis of the solvation contributions shows that two major effects neglected when torsion parameters are derived in vacuo are (i) conformation-dependent solute polarization and (ii) solvation of conformation-dependent charge distribution. Using the glycosidic torsion as an example, we demonstrate that the corresponding correction for the torsion potential is substantial and important. Our approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models, such as TIPnP or SPC/E, or with continuum solvent models. Differences between our model and the previously suggested solvation models are discussed. Improvements were demonstrated for the latest AMBER RNA chi(OL3) parameters derived with inclusion of solvent effects in a previous publication (Zgarbova et al. J. Chem. Theory Comput. 2011, 7, 2886). The described procedure may help to provide consistently better force field parameters than the currently used parametrization approaches. A procedure for deriving force field torsion parameters including certain previously neglected solvation effects is suggested. In contrast to the conventional in vacuo approaches, the dihedral parameters are obtained from the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. An analysis of the solvation contributions shows that two major effects neglected when torsion parameters are derived in vacuo are (i) conformation-dependent solute polarization and (ii) solvation of conformation-dependent charge distribution. Using the glycosidic torsion as an example, we demonstrate that the corresponding correction for the torsion potential is substantial and important. Our approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models, such as TIPnP or SPC/E, or with continuum solvent models. Differences between our model and the previously suggested solvation models are discussed. Improvements were demonstrated for the latest AMBER RNA chi(OL3) parameters derived with inclusion of solvent effects in a previous publication (Zgarbova et al. J. Chem. Theory Comput. 2011, 7, 2886). The described procedure may help to provide consistently better force field parameters than the currently used parametrization approaches. (en)
Title	A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects (en)
skos:prefLabel	A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects (en)
skos:notation	RIV/61989592:15310/12:33142606!RIV13-MSM-15310___
http://linked.open...avai/predkladatel	Přírodovědecká fakulta
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(GA203/09/1476), P(GAP208/10/1742), P(GAP208/11/1822), P(GAP208/12/1878), P(GBP305/12/G034), P(GD203/09/H046), Z(AV0Z50040702)
http://linked.open...iv/cisloPeriodika	9
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Otyepka, Michal Jurečka, Petr Zgarbová, Marie
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	Univerzita Palackého v Olomouci / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	120463
http://linked.open...ai/riv/idVysledku	RIV/61989592:15310/12:33142606
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	parametrization; basis-sets; resp model; atomic charges; ionic-solutions; continuum model; anisotropic dielectrics; free-energy; nucleic-acids; molecular-orbital methods (en)
http://linked.open.../riv/klicoveSlovo	basis-sets anisotropic dielectrics atomic charges continuum model ionic-solutions molecular-orbital methods resp model parametrization nucleic-acids free-energy
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[06DC60303D18]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Molecules on the Surfaces of Carbon Nanostructures Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach Centre for RNA Biology Central european institute of technology Regional Centre of Advanced Technologies and Materials Research team development of the Regional Centre of Advanced Technologies and Materials Structural dynamics, molecular interactions and function of key RNA motifs Biochemistry on the crossroad from in silico to in vitro Structure and dynamics of DNA. Advanced computational studies.
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	8
http://linked.open...iv/tvurceVysledku	Otyepka, Michal Šponer, Jiří Jurečka, Petr Luque, F Javier Zgarbová, Marie
http://linked.open...ain/vavai/riv/wos	000308830700027
http://linked.open...n/vavai/riv/zamer	Genome and epigenome: 1D and 3D Structure, Dynamics, Interactions with Proteins and Functions
issn	1549-9618
number of pages	11 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct3001987
http://localhost/t...ganizacniJednotka	15310
is http://linked.open...avai/riv/vysledek of	A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects

Faceted Search & Find service v1.16.118 as of Jun 21 2024

Alternative Linked Data Documents: ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3240 as of Jun 21 2024, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (126 GB total memory, 58 GB memory in use)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software