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Polish Academy of Sciences

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Simón Poblete


Recent publications
1.  Cofas Vargas L.F., Azevedo Rodrigo M., Poblete S., Chwastyk M., Poma Bernaola A.M., The GōMartini Approach: Revisiting the Concept of Contact Maps and the Modelling of Protein Complexes, ACTA PHYSICA POLONICA A, ISSN: 0587-4246, DOI: 10.12693/APhysPolA.145.S9, Vol.145, No.3, pp.S9-S20, 2024

Abstract:
We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g., distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust Gō-Martini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based Gō--like approach to the study of protein–sugar complexes, and the limitations of this approach are also discussed. The Gō-Martini approach was first introduced by Poma et al. (J. Chem. Theory Comput. 13, 1366 (2017)) in Martini 2 force field, and recently, it has gained the status of gold standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support for this approach in the context of the biophysical community.

Keywords:
Martini 3,Structure-based coarse-graining,SMFS,biomolecules,GoMartini

Affiliations:
Cofas Vargas L.F. - other affiliation
Azevedo Rodrigo M. - other affiliation
Poblete S. - other affiliation
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Poma Bernaola A.M. - other affiliation
2.  Poblete S., Pantano S., Okazaki K., Liang Z., Kremer K., Poma Adolfo B., Editorial: Recent advances in computational modelling of biomolecular complexes, Frontiers in Chemistry, ISSN: 2296-2646, DOI: 10.3389/fchem.2023.1200409, Vol.11, pp.1200409-1-3, 2023, EDITORIAL

Keywords:
coarse-grained method, machine learning, multiscale approach, biopolymers, aggregation, GōMartini approach, Martini 3, nanomechanics

Affiliations:
Poblete S. - other affiliation
Pantano S. - other affiliation
Okazaki K. - other affiliation
Liang Z. - other affiliation
Kremer K. - other affiliation
Poma Adolfo B. - IPPT PAN

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