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Rok 2024

Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales
Publikacja
- C. Czaplewski
- P. Czarnul
- H. Krawczyk
- A. Lipska
- E. Lubecka
- K. Ocetkiewicz
- J. Proficz
- A. Sieradzan
- R. Ślusarz
- J. Liwo
- BIOPHYSICAL JOURNAL - Rok 2024
Coarse-grained models are nowadays extensively used in biomolecular simulations owing to the tremendous extension of size- and time-scale of simulations. The physics-based UNRES (UNited RESidue) model of proteins developed in our laboratory has only two interaction sites per amino-acid residue (united peptide groups and united side chains) and implicit solvent. However, owing to rigorous physics-based derivation, which enabled...

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Rok 2023

Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
Publikacja
- A. Lipska
- A. Sieradzan
- C. Czaplewski
- A. D. Lipińska
- K. Ocetkiewicz
- J. Proficz
- P. Czarnul
- H. Krawczyk
- J. Liwo
- JOURNAL OF COMPUTATIONAL CHEMISTRY - Rok 2023
The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...

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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
Publikacja
- BIOINFORMATICS - Rok 2023
The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...

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