Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
The SARS-CoV-2 Spike variant D614G favors an open conformational state
The COVID-19 global pandemic is an international health emergency. It is caused by the
SARS-CoV-2 virus, which binds with its trimeric Spike protein to the ACE2 receptor in the …
SARS-CoV-2 virus, which binds with its trimeric Spike protein to the ACE2 receptor in the …
Model parameters for simulation of physiological lipids
RD Hills Jr, N McGlinchey - Journal of computational chemistry, 2016 - Wiley Online Library
Coarse grain simulation of proteins in their physiological membrane environment can offer
insight across timescales, but requires a comprehensive force field. Parameters are …
insight across timescales, but requires a comprehensive force field. Parameters are …
Necessity of high‐resolution for coarse‐grained modeling of flexible proteins
The popular MARTINI coarse‐grained (CG) force field requires the protein structure to be
fixed, and is unsuitable for simulating dynamic processes such as protein folding. Here, we …
fixed, and is unsuitable for simulating dynamic processes such as protein folding. Here, we …
[PDF][PDF] Simulation of lipid-protein interactions with the CgProt force field
J Fosso-Tande, C Black, SG Aller, L Lu… - AIMS Molecular …, 2017 - par.nsf.gov
Simulation of lipid-protein interactions with the CgProt force field Page 1 AIMS Molecular
Science, 4 (3):352-369. DOI: 10.3934/molsci.2017.3.352 Received 13 July 2017, Accepted 17 …
Science, 4 (3):352-369. DOI: 10.3934/molsci.2017.3.352 Received 13 July 2017, Accepted 17 …
Refining amino acid hydrophobicity for dynamics simulation of membrane proteins
RD Hills Jr - PeerJ, 2018 - peerj.com
Coarse-grained (CG) models have been successful in simulating the chemical properties of
lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular …
lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular …