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rdf:type
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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)
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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)
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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)
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skos:notation
| - RIV/61388963:_____/11:00368013!RIV12-AV0-61388963
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http://linked.open...avai/riv/aktivita
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http://linked.open...avai/riv/aktivity
| - P(1M0508), P(GAP208/11/0295), P(LC512), Z(AV0Z40550506)
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http://linked.open...iv/cisloPeriodika
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http://linked.open...vai/riv/dodaniDat
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http://linked.open...aciTvurceVysledku
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http://linked.open.../riv/druhVysledku
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http://linked.open...iv/duvernostUdaju
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http://linked.open...titaPredkladatele
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http://linked.open...dnocenehoVysledku
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http://linked.open...ai/riv/idVysledku
| - RIV/61388963:_____/11:00368013
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http://linked.open...riv/jazykVysledku
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http://linked.open.../riv/klicovaSlova
| - HIV-1 protease inhibition; protonation; QM/MM calculations (en)
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http://linked.open.../riv/klicoveSlovo
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http://linked.open...odStatuVydavatele
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http://linked.open...ontrolniKodProRIV
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http://linked.open...i/riv/nazevZdroje
| - Collection of Czechoslovak Chemical Communications
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http://linked.open...in/vavai/riv/obor
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http://linked.open...ichTvurcuVysledku
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http://linked.open...cetTvurcuVysledku
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http://linked.open...vavai/riv/projekt
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http://linked.open...UplatneniVysledku
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http://linked.open...v/svazekPeriodika
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http://linked.open...iv/tvurceVysledku
| - Hobza, Pavel
- Lepšík, Martin
- Řezáč, Jan
- Fanfrlík, Jindřich
- Přenosil, Ondřej
- Granatier, Jaroslav
- Pecina, Adam
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http://linked.open...ain/vavai/riv/wos
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http://linked.open...n/vavai/riv/zamer
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issn
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number of pages
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http://bibframe.org/vocab/doi
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