Research Group on Quantum Chemistry
Applied to Biological Systems
Gerd Bruno Rocha
DQ - CCEN - UFPB - Brazil
PRIMoRDiA (PRIMoRDiA Macromolecular Reactivity Descriptors Access) is a shared-memory parallel software written in C++ with functions for parsing the output of many traditional quantum chemical programs, store and manipulate molecular information, generate and write files with scalar fields containing electron density, molecular orbitals, and many variations of reactivity descriptors. Using PRIMoRDiA the user will be able to generate plenty of descriptors for evaluating global and local reactivities for small and large molecules, including proteins and DNA fragments. PRIMoRDiA supports the main reactivity descriptors from the Conceptual Density Functional Theory, the most famous and used reactivity theory, which works using response variables of the molecular electronic structure, as also other electrostatics properties. Our program supports plenty of methods of calculating Fukui functions, and its output can be written containing volumetric data to be rendered and/or a list of reactivity values for atoms and/or protein residues.
PRIMoRDiA: A Software to Explore Reactivity and Electronic Structure in Large Biomolecules
Author(s): Grillo, Igor Barden ; Urquiza-Carvalho, Gabriel A. ; Rocha, Gerd Bruno
Source: Journal of Chemical Information and Modeling
At the following website (PRIMoRDiA website), users will find a guide that resumes:
1. General usage
2. Specific options
3. Information needed from the quantum mechanical packages output (how to build their input files)
4. Input format and reactivity descriptors options.
5. List of generated files and descriptors.
6. How to work with the generated scripts for using graphical packages.
Publications that use PRIMoRDiA:
A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers
Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors
Elucidating Enzymatic Catalysis Using Fast Quantum Chemical Descriptors: DOI: 10.1021/acs.jcim.9b00860
Semiempirical methods do Fukui functions: Unlocking a modeling framework for biosystems: DOI: 10.1002/jcc.26148.