PRIMoRDiA: A Software to Explore Reactivity and Electronic Structure in Large Biomolecules.
J Chem Inf Model
; 60(12): 5885-5890, 2020 12 28.
Article
in English
| MEDLINE | ID: covidwho-1065775
ABSTRACT
Plenty of enzymes with structural data do not have their mechanism of catalysis elucidated. Reactivity descriptors, theoretical quantities generated from resolved electronic structure, provide a way to predict and rationalize chemical processes of such systems. In this Application Note, we present PRIMoRDiA (PRIMoRDiA Macromolecular Reactivity Descriptors Access), a software built to calculate the reactivity descriptors of large biosystems by employing an efficient and accurate treatment of the large output files produced by quantum chemistry packages. Here, we show the general implementation details and the software main features. Calculated descriptors were applied for a set of enzymatic systems in order to show their relevance for biological studies and the software potential for use in large scale. Also, we test PRIMoRDiA to aid in the interaction depiction between the SARS-CoV-2 main protease and a potential inhibitor.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Computer Simulation
/
Software
/
Models, Molecular
Type of study:
Prognostic study
Limits:
Humans
Language:
English
Journal:
J Chem Inf Model
Journal subject:
Medical Informatics
/
Chemistry
Year:
2020
Document Type:
Article
Affiliation country:
Acs.jcim.0c00655
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