TY - JOUR
T1 - ELViM
T2 - Exploring Biomolecular Energy Landscapes through Multidimensional Visualization
AU - Viegas, Rafael Giordano
AU - Martins, Ingrid B.S.
AU - Sanches, Murilo Nogueira
AU - Oliveira Junior, Antonio B.
AU - de Camargo, Juliana B.
AU - Paulovich, Fernando V.
AU - Leite, Vitor B.P.
PY - 2024/4/22
Y1 - 2024/4/22
N2 - Molecular dynamics (MD) simulations provide a powerful means of exploring the dynamic behavior of biomolecular systems at the atomic level. However, analyzing the vast data sets generated by MD simulations poses significant challenges. This article discusses the energy landscape visualization method (ELViM), a multidimensional reduction technique inspired by the energy landscape theory. ELViM transcends one-dimensional representations, offering a comprehensive analysis of the effective conformational phase space without the need for predefined reaction coordinates. We apply the ELViM to study the folding landscape of the antimicrobial peptide Polybia-MP1, showcasing its versatility in capturing complex biomolecular dynamics. Using dissimilarity matrices and a force-scheme approach, the ELViM provides intuitive visualizations, revealing structural correlations and local conformational signatures. The method is demonstrated to be adaptable, robust, and applicable to various biomolecular systems.
AB - Molecular dynamics (MD) simulations provide a powerful means of exploring the dynamic behavior of biomolecular systems at the atomic level. However, analyzing the vast data sets generated by MD simulations poses significant challenges. This article discusses the energy landscape visualization method (ELViM), a multidimensional reduction technique inspired by the energy landscape theory. ELViM transcends one-dimensional representations, offering a comprehensive analysis of the effective conformational phase space without the need for predefined reaction coordinates. We apply the ELViM to study the folding landscape of the antimicrobial peptide Polybia-MP1, showcasing its versatility in capturing complex biomolecular dynamics. Using dissimilarity matrices and a force-scheme approach, the ELViM provides intuitive visualizations, revealing structural correlations and local conformational signatures. The method is demonstrated to be adaptable, robust, and applicable to various biomolecular systems.
UR - http://www.scopus.com/inward/record.url?scp=85188475131&partnerID=8YFLogxK
U2 - 10.1021/acs.jcim.4c00034
DO - 10.1021/acs.jcim.4c00034
M3 - Article
C2 - 38506664
AN - SCOPUS:85188475131
SN - 1549-9596
VL - 64
SP - 3443
EP - 3450
JO - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
IS - 8
ER -