Quantum Mechanics in Biomolecular Simulations: Benefits and Cost-Reduction Strategies for Integrated QM/MM Approaches

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F62690094%3A18470%2F25%3A50023138" target="_blank" >RIV/62690094:18470/25:50023138 - isvavai.cz</a>

Výsledek na webu

<a href="https://rvq.sbq.org.br/pdf/CMQ2025-5043" target="_blank" >https://rvq.sbq.org.br/pdf/CMQ2025-5043</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.21577/1984-6835.20250079" target="_blank" >10.21577/1984-6835.20250079</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Quantum Mechanics in Biomolecular Simulations: Benefits and Cost-Reduction Strategies for Integrated QM/MM Approaches

Popis výsledku v původním jazyce

Quantum calculations play a fundamental role in understanding biological systems at the atomic level, as they allow detailed investigation of electronic interactions, enzymatic mechanisms, and molecular recognition processes. However, the direct application of these methods to large biomolecules is limited by the high computational cost involved. An efficient alternative consists of combining classical Molecular Mechanics (MM) simulations, such as molecular dynamics, with quantum mechanical (QM) methods, enabling a more comprehensive multiscale description. This hybrid approach, however, introduces another challenge: classical simulations generate a very large number of conformations, which makes it impractical to perform quantum calculations on every frame. Therefore, the efficiency of this strategy depends on selecting a reduced and representative set of structures to be analyzed in subsequent quantum stages. In this mini-review, we present three complementary methods to achieve this selection: (1) Clustering, (2) Statistical Inefficiency (SI), and (3) Optimal Wavelet Signal Compression Analysis (OWSCA). This filtering step makes it possible to explore quantum effects with high accuracy without compromising conformational representativeness, drastically reducing the computational cost and expanding the applicability of a sequential workflow of hybrid QM/ MM methodologies to the study of complex biological systems. © 2025 Sociedade Brasileira de Química.

Název v anglickém jazyce

Quantum Mechanics in Biomolecular Simulations: Benefits and Cost-Reduction Strategies for Integrated QM/MM Approaches

Popis výsledku anglicky

Quantum calculations play a fundamental role in understanding biological systems at the atomic level, as they allow detailed investigation of electronic interactions, enzymatic mechanisms, and molecular recognition processes. However, the direct application of these methods to large biomolecules is limited by the high computational cost involved. An efficient alternative consists of combining classical Molecular Mechanics (MM) simulations, such as molecular dynamics, with quantum mechanical (QM) methods, enabling a more comprehensive multiscale description. This hybrid approach, however, introduces another challenge: classical simulations generate a very large number of conformations, which makes it impractical to perform quantum calculations on every frame. Therefore, the efficiency of this strategy depends on selecting a reduced and representative set of structures to be analyzed in subsequent quantum stages. In this mini-review, we present three complementary methods to achieve this selection: (1) Clustering, (2) Statistical Inefficiency (SI), and (3) Optimal Wavelet Signal Compression Analysis (OWSCA). This filtering step makes it possible to explore quantum effects with high accuracy without compromising conformational representativeness, drastically reducing the computational cost and expanding the applicability of a sequential workflow of hybrid QM/ MM methodologies to the study of complex biological systems. © 2025 Sociedade Brasileira de Química.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10406 - Analytical chemistry

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Revista Virtual de Química

ISSN

1984-6835

e-ISSN

1984-6835

Svazek periodika

17

Číslo periodika v rámci svazku

6

Stát vydavatele periodika

BR - Brazilská federativní republika

Počet stran výsledku

6

Strana od-do

846-851

Kód UT WoS článku

001668935500012

EID výsledku v databázi Scopus

2-s2.0-105027665175