Bottom-up coarse-graining: Principles and perspectives

J Jin, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

TorchMD: A deep learning framework for molecular simulations

S Doerr, M Majewski, A Pérez, A Kramer… - Journal of chemical …, 2021 - ACS Publications
Molecular dynamics simulations provide a mechanistic description of molecules by relying
on empirical potentials. The quality and transferability of such potentials can be improved …

[HTML][HTML] Peptide and peptide-based inhibitors of SARS-CoV-2 entry

D Schütz, YB Ruiz-Blanco, J Münch, F Kirchhoff… - Advanced drug delivery …, 2020 - Elsevier
To date, no effective vaccines or therapies are available against the severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), the causative pandemic agent of the coronavirus …

Machine learning coarse-grained potentials of protein thermodynamics

M Majewski, A Pérez, P Thölke, S Doerr… - Nature …, 2023 - nature.com
A generalized understanding of protein dynamics is an unsolved scientific problem, the
solution of which is critical to the interpretation of the structure-function relationships that …

Pragmatic coarse-graining of proteins: models and applications

L Borges-Araújo, I Patmanidis, AP Singh… - Journal of Chemical …, 2023 - ACS Publications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

Backmapping triangulated surfaces to coarse-grained membrane models

W Pezeshkian, M König, TA Wassenaar… - Nature …, 2020 - nature.com
Many biological processes involve large-scale changes in membrane shape. Computer
simulations of these processes are challenging since they occur across a wide range of …

Advances in the study of supercooled water

P Gallo, J Bachler, LE Bove, R Böhmer… - The European Physical …, 2021 - Springer
In this review, we report recent progress in the field of supercooled water. Due to its
uniqueness, water presents numerous anomalies with respect to most simple liquids …

Secreted Aspartyl Proteinases Targeted Multi-Epitope Vaccine Design for Candida dubliniensis Using Immunoinformatics

N Akhtar, JSL Magdaleno, S Ranjan, AK Wani… - Vaccines, 2023 - mdpi.com
Candida dubliniensis is an opportunistic pathogen associated with oral and invasive fungal
infections in immune-compromised individuals. Furthermore, the emergence of C …