Modeling the structure, dynamics, and transformations of proteins with the UNRES force field
… of the UNRES package have been originally written in FORTRAN 77; recently, a FORTRAN
90 version has been released [58]. To store coordinates from MD/MREMD, this new version …
90 version has been released [58]. To store coordinates from MD/MREMD, this new version …
Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field
AV Rojas, GG Maisuradze, HA Scheraga… - Computer Simulations of …, 2022 - Springer
… package includes the standard version of UNRES (with which the simulations reported in this
chapter were performed) and the latest … original FORTRAN 77 and the newer FORTRAN 90 …
chapter were performed) and the latest … original FORTRAN 77 and the newer FORTRAN 90 …
Introduction of phosphorylated residues into the UNRES coarse-grained model: toward modeling of signaling processes
AK Sieradzan, M Bogunia, P Mech… - The Journal of …, 2019 - ACS Publications
… The all-atom force fields enable us to study the systems … -based coarse-grained UNRES
force field to treat systems with … new potentials were subsequently introduced into UNRES …
force field to treat systems with … new potentials were subsequently introduced into UNRES …
[HTML][HTML] Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
KM Ocetkiewicz, C Czaplewski, H Krawczyk… - Computer Physics …, 2024 - Elsevier
… of UNRES. This difference often means that the simulations are doable with the new version
… : the model adopted within UNRES, an overview of the UNRES simulator as well as state-of-…
… : the model adopted within UNRES, an overview of the UNRES simulator as well as state-of-…
A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the …
… coarse-grained force field, such as UNRES [44], a component of the UNICORN package [45],
or … are based on three force fields: the all-atom ff19SB force field coupled with the four-point …
or … are based on three force fields: the all-atom ff19SB force field coupled with the four-point …
Sampling of the conformational landscape of small proteins with Monte Carlo methods
… and standard all-atom force fields. We demonstrate extensive … -of-the-art intramolecular
force field can be combined with an … using different MC program packages developed to model …
force field can be combined with an … using different MC program packages developed to model …
[HTML][HTML] Computational reconstruction of atomistic protein structures from coarse-grained models
AE Badaczewska-Dawid, A Kolinski… - Computational and …, 2020 - Elsevier
… Uses a force field with the concept of hydropathic interactions (HINT) as its noncovalent force
field and exhaustive enumeration for optimization. The method uses coordinate data for the …
field and exhaustive enumeration for optimization. The method uses coordinate data for the …
100 Years of the Lennard-Jones Potential
P Schwerdtfeger, DJ Wales - Journal of Chemical Theory and …, 2024 - ACS Publications
… We only mention that different force fields can lead to rather different tertiary structures, (216)
and one has to carefully test the parametrization for specific biochemical applications. On a …
and one has to carefully test the parametrization for specific biochemical applications. On a …
Inferences on the 2021 ongoing volcanic unrest at Vulcano Island (Italy) through a comprehensive multidisciplinary surveillance network
… In September 2021, the La Fossa crater at Vulcano, in Italy, entered a new phase of unrest.
… different phases of the unrest, thus allowing a consistent evaluation of the multiple hazards. …
… different phases of the unrest, thus allowing a consistent evaluation of the multiple hazards. …
KORP-PL: a coarse-grained knowledge-based scoring function for protein–ligand interactions
… To evaluate the performance of KORP-PL in large-scale virtual screening tasks, we have
assessed it on 90 targets from the DUD-E benchmark. As shown in Table 1 and Figure 5, KORP…
assessed it on 90 targets from the DUD-E benchmark. As shown in Table 1 and Figure 5, KORP…