About: On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes

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About: On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	A novel computational protocol for studying protonation in protein/ligand complexes is presented. We use a QM/MM approach in which the large QM part (the ligand and the active site) are treated using the corrected semiempirical method PM6-DH2, while the MM part (the rest of the protein and the surrounding solvent) are calculated using MM/GB method. This approach is applied to two model systems, the carboxylate pairs in HIV-1 protease/inhibitor complexes. The computationally more costly DFT optimizations are performed for a smaller QM part as a check of the correctness. Proton transfer (PT) phenomena occur at both the PM6-D2 and DFT levels, which underlines the requirement for a QM approach. The barriers of PT are checked in model carboxylic acid pairs using the highly accurate MP2 and CCSD(T) values. An important result of this study is the fine-tuning of the protocol which can be used in further applications; its limitations are also shown, pointing to future developments. A novel computational protocol for studying protonation in protein/ligand complexes is presented. We use a QM/MM approach in which the large QM part (the ligand and the active site) are treated using the corrected semiempirical method PM6-DH2, while the MM part (the rest of the protein and the surrounding solvent) are calculated using MM/GB method. This approach is applied to two model systems, the carboxylate pairs in HIV-1 protease/inhibitor complexes. The computationally more costly DFT optimizations are performed for a smaller QM part as a check of the correctness. Proton transfer (PT) phenomena occur at both the PM6-D2 and DFT levels, which underlines the requirement for a QM approach. The barriers of PT are checked in model carboxylic acid pairs using the highly accurate MP2 and CCSD(T) values. An important result of this study is the fine-tuning of the protocol which can be used in further applications; its limitations are also shown, pointing to future developments. (en)
Title	On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes (en)
skos:prefLabel	On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes (en)
skos:notation	RIV/61388963:_____/11:00368013!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(1M0508), P(GAP208/11/0295), P(LC512), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	5
http://linked.open...vai/riv/dodaniDat	2012
http://linked.open...aciTvurceVysledku	Řezáč, Jan Hobza, Pavel Fanfrlík, Jindřich Granatier, Jaroslav Lepšík, Martin Přenosil, Ondřej Pecina, Adam
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	218275
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/11:00368013
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	HIV-1 protease inhibition; protonation; QM/MM calculations (en)
http://linked.open.../riv/klicoveSlovo	HIV-1 protease inhibition protonation QM/MM calculations
http://linked.open...odStatuVydavatele	CZ - Česká republika
http://linked.open...ontrolniKodProRIV	[B24B167C4870]
http://linked.open...i/riv/nazevZdroje	Collection of Czechoslovak Chemical Communications
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	7 (xsd:int)
http://linked.open...cetTvurcuVysledku	7 (xsd:int)
http://linked.open...vavai/riv/projekt	In silico drug design based on advanced semiempirical quantum mechanical methods accurately describing noncovalent interactions New Antivirals and Antineoplastics Center for biomolecules and complex molecular systems
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	76
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Lepšík, Martin Řezáč, Jan Fanfrlík, Jindřich Přenosil, Ondřej Granatier, Jaroslav Pecina, Adam
http://linked.open...ain/vavai/riv/wos	000290280100009
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	0010-0765
number of pages	23 (xsd:int)
http://bibframe.org/vocab/doi	10.1135/cccc2011035
is http://linked.open...avai/riv/vysledek of	On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes

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