A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems.

Henrique S Fernandes, Nuno M F S A Cerqueira, Sérgio F Sousa, André Melo

Abstract read

In one paragraph

Article in Molecules (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

4 authors.

Henrique S FernandesAssociate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal.ORCID 0000-0002-9280-1838

Nuno M F S A CerqueiraAssociate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal.

Sérgio F SousaAssociate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal.ORCID 0000-0002-6560-5284

André MeloFaculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 1021 1055, 4169-007 Porto, Portugal.

Funding

Fundação para a Ciência e Tecnologia This work was supported by the Applied Molecular Biosciences Unit-UCIBIO, which is financed by national funds from FCT (UIDP/04378/2020 and UIDB/04378/2020). SFS acknowledges FCT for his grant 2020.01423.CEECIND. Some of the calculations were produced wit

6 · The paper itself

Abstract

The partitioning of the molecular mechanics (MM) energy in calculations involving biomolecular systems is important to identify the source of major stabilizing interactions, e.g., in ligand-protein interactions, or to identify residues with considerable contributions in hybrid multiscale calculations, i.e., quantum mechanics/molecular mechanics (QM/MM). Here, we describe Energy Split, a software program to calculate MM energy partitioning considering the AMBER Hamiltonian and parameters. Energy Split includes a graphical interface plugin for VMD to facilitate the selection of atoms and molecules belonging to each part of the system. Energy Split is freely available at or can be easily installed through the VMD Store.

Indexed as

Molecular Dynamics SimulationQuantum TheoryLigandsPhysical PhenomenaSoftwareLigandsAMBERenergy partitionmolecular interactionmolecular mechanics

Identifiers

PMID36080291

DOI10.3390/molecules27175524

PMCPMC9458121

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LicenceCC BY

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