About: Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors

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

About: Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors 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	Abstract A semiempirical quantum mechanical PM6-DH2 method accurately covering the dispersion interaction and H-bonding was used to score fifteen structurally diverse CDK2 inhibitors. The geometries of all the complexes were taken from the X-ray structures and were reoptimised by the PM6-DH2 method in continuum water. The total scoring function was constructed as an estimate of the binding free energy, i.e., as a sum of the interaction enthalpy, interaction entropy and the corrections for the inhibitor desolvation and deformation energies. The applied scoring function contains a clear thermodynamical terms and does not involve any adjustable empirical parameter. The best correlations with the experimental inhibition constants (ln Ki) were found for bare interaction enthalpy (r2 = 0.87) and interaction enthalpy corrected for ligand desolvation and deformation energies (r2 = 0.77); when the entropic term was considered, however, the correlation becomes worse but still acceptable. Abstract A semiempirical quantum mechanical PM6-DH2 method accurately covering the dispersion interaction and H-bonding was used to score fifteen structurally diverse CDK2 inhibitors. The geometries of all the complexes were taken from the X-ray structures and were reoptimised by the PM6-DH2 method in continuum water. The total scoring function was constructed as an estimate of the binding free energy, i.e., as a sum of the interaction enthalpy, interaction entropy and the corrections for the inhibitor desolvation and deformation energies. The applied scoring function contains a clear thermodynamical terms and does not involve any adjustable empirical parameter. The best correlations with the experimental inhibition constants (ln Ki) were found for bare interaction enthalpy (r2 = 0.87) and interaction enthalpy corrected for ligand desolvation and deformation energies (r2 = 0.77); when the entropic term was considered, however, the correlation becomes worse but still acceptable. (en)
Title	Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors (en)
skos:prefLabel	Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors (en)
skos:notation	RIV/61388963:_____/11:00360708!RIV12-AV0-61388963
http://linked.open...avai/predkladatel	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(ED2.1.00/03.0058), P(GAP208/11/0295), P(LC512), Z(AV0Z40550506), Z(MSM6198959216)
http://linked.open...iv/cisloPeriodika	3
http://linked.open...vai/riv/dodaniDat	2012
http://linked.open...aciTvurceVysledku	Řezáč, Jan Hobza, Pavel Fanfrlík, Jindřich Dobeš, Petr
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	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	235780
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/11:00360708
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	CDK2; semiempirical quantum mechanical method PM6-DH2; drug design (en)
http://linked.open.../riv/klicoveSlovo	CDK2 semiempirical quantum mechanical method PM6-DH2 drug design
http://linked.open...odStatuVydavatele	NL - Nizozemsko
http://linked.open...ontrolniKodProRIV	[BFBE4912CBA1]
http://linked.open...i/riv/nazevZdroje	Journal of Computer-Aided Molecular Design
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	In silico drug design based on advanced semiempirical quantum mechanical methods accurately describing noncovalent interactions Regional Centre of Advanced Technologies and Materials Center for biomolecules and complex molecular systems
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	25
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Řezáč, Jan Dobeš, Petr Fanfrlík, Jindřich Otyepka, M.
http://linked.open...ain/vavai/riv/wos	000288179000005
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství Modulation of signalling and regulatory pathways in normal and cancer cells
issn	0920-654X
number of pages	12 (xsd:int)
http://bibframe.org/vocab/doi	10.1007/s10822-011-9413-5
is http://linked.open...avai/riv/vysledek of	Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors

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, 48 GB memory in use)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software