Two decades of Martini: Better beads, broader scope
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 …
been around for nearly two decades. Originally developed for lipid‐based systems by the …
[HTML][HTML] Molecular modeling in drug discovery
With the financial requirements and high time associated with bringing a commercial drug to
the market, the application of computer-aided drug design has been recognized as a …
the market, the application of computer-aided drug design has been recognized as a …
Martini 3: a general purpose force field for coarse-grained molecular dynamics
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …
Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution
FE Thomasen, T Skaalum, A Kumar… - Nature …, 2024 - nature.com
Multidomain proteins with flexible linkers and disordered regions play important roles in
many cellular processes, but characterizing their conformational ensembles is difficult. We …
many cellular processes, but characterizing their conformational ensembles is difficult. We …
PyLipID: a python package for analysis of protein–lipid interactions from molecular dynamics simulations
Lipids play important modulatory and structural roles for membrane proteins. Molecular
dynamics simulations are frequently used to provide insights into the nature of these protein …
dynamics simulations are frequently used to provide insights into the nature of these protein …
Machine learned coarse-grained protein force-fields: Are we there yet?
The successful recent application of machine learning methods to scientific problems
includes the learning of flexible and accurate atomic-level force-fields for materials and …
includes the learning of flexible and accurate atomic-level force-fields for materials and …
Artificial intelligence and machine learning approaches for drug design: challenges and opportunities for the pharmaceutical industries
C Selvaraj, I Chandra, SK Singh - Molecular diversity, 2021 - Springer
The global spread of COVID-19 has raised the importance of pharmaceutical drug
development as intractable and hot research. Developing new drug molecules to overcome …
development as intractable and hot research. Developing new drug molecules to overcome …
Martini 3 coarse‐grained force field: small molecules
The recent re‐parametrization of the Martini coarse‐grained force field, Martini 3, improved
the accuracy of the model in predicting molecular packing and interactions in molecular …
the accuracy of the model in predicting molecular packing and interactions in molecular …
Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
Martini 3 coarse-grained force field for carbohydrates
F Grünewald, MH Punt, EE Jefferys… - Journal of Chemical …, 2022 - ACS Publications
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for
biomolecular simulations. Due to the improved interaction balance, it allows for a more …
biomolecular simulations. Due to the improved interaction balance, it allows for a more …