Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F16%3A00088632" target="_blank" >RIV/00216224:14740/16:00088632 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1021/acs.jctc.6b00531" target="_blank" >http://dx.doi.org/10.1021/acs.jctc.6b00531</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jctc.6b00531" target="_blank" >10.1021/acs.jctc.6b00531</a>
Alternative languages
Result language
angličtina
Original language name
Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2
Original language description
Hybrid QM/MM computational studies can provide invaluable insight into the mechanisms of enzymatic reactions that can be exploited for rational drug design. Various approaches are available for such studies. However, their strengths and weaknesses may not be immediately apparent. Using the retaining glycosyltransferase ppGalNAcT2 as a case study, we compare different methodologies used to obtain reaction paths and transition state information. Ab Initio MD using CPMD coupled with the String Method is used to derive the minimum free energy reaction path. The geometrical features of the free energy path, especially around the transition state, agree with the minimum potential energy path obtained by the much less computationally expensive Nudged Elastic Band method. The barrier energy, however, differs by 8 kcal/mol.
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2016
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Theory and Computation
ISSN
1549-9618
e-ISSN
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Volume of the periodical
12
Issue of the periodical within the volume
12
Country of publishing house
US - UNITED STATES
Number of pages
15
Pages from-to
6062-6076
UT code for WoS article
000389866500033
EID of the result in the Scopus database
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