we present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein–ligand interactions of small drug-like molecules. Remarkably, we achieve high accuracy without the need of any a priori knowledge of binding pockets or pathways...
Protein-Ligand Binding Simulation with the Martini Coarse-Grained Force Fieldelectrochemicalgraphenemagnetic beadsgold nanoparticleshorseradish peroxidaseBiosynthesis of metal clusters for the nitrogenase component proteins NifH and NifDK involves electron donation events. Yet, electron donors specific to the ...
Multidomain proteins with flexible linkers and disordered regions play important roles in many cellular processes, but characterizing their conformational ensembles is difficult. We have previously shown that the coarse-grained model, Martini 3, produces
the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training...
the work by Hills et al.30has made significant strides towards creating a transferable bottom-up coarse-grained potential for the simulation of proteins, contributing valuable insights to the field. Popular CG approaches include structure-based models31, MARTINI32,33, CABS34, AWSEM35, and Rosetta36...
Club-martini: selecting favourable interactions amongst available candi- dates, a coarse-grained simulation approach to scoring docking decoys. PLoS ONE. 2016;11(5):e0155251. 16. Zhang B, Li J, Quan L, Chen Y, Lü Q. Sequence-based prediction of protein-protein interaction sites by ...
A new feature in NanoModeler enables the creation and parametrization of monolayer-protected metal nanoparticles (NPs) with a coarse-grained (CG) resolution. Our original methodology has been expanded to accommodate nanoparticles of eight diverse shapes, each potentially constructed from up to 800,000...
For example, in certain coarse-grained (CG) biomolecular force fields, such as Martini [22], groups of atoms are modelled as a single bead or particle, allowing faster sampling of protein–lipid configurations compared with atomistic simulations. CG simulations have been successfully applied to ...
et al. The MARTINI coarse-grained force field: extension to proteins. J. Chem. Theory Comput. 4, 819–834 (2008). Article CAS PubMed Google Scholar Tozzini, V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15, 144–150 (2005). Article CAS PubMed Google Scholar ...
et al. The MARTINI coarse-grained force field: extension to proteins. J. Chem. Theory Comput. 4, 819–834 (2008). Article CAS PubMed Google Scholar Tozzini, V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15, 144–150 (2005). Article CAS PubMed Google Scholar ...