Modeling the structure, dynamics, and transformations of proteins with the UNRES force field
… It should be noted that the U SCiSCj potentials contain contributions from … (multibody)
terms that account for the coupling between the backbone-local and backbone-electrostatic …
terms that account for the coupling between the backbone-local and backbone-electrostatic …
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
… that contribute to local-interaction energies within the backbone and … -based OPEP force
field 3 also has similar multibody terms … based on the cooperativity of electrostatic interactions. …
field 3 also has similar multibody terms … based on the cooperativity of electrostatic interactions. …
Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of …
A Liwo, C Czaplewski - The Journal of chemical physics, 2020 - pubs.aip.org
… dependence on orientation and multibody energy terms that … are partitioned between the
backbone and side groups; we … the backbone-local and backbone-electrostatic interactions 17…
backbone and side groups; we … the backbone-local and backbone-electrostatic interactions 17…
Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches
AG Lipska, AK Sieradzan, S Atmaca… - The Journal of …, 2023 - ACS Publications
… unable to parametrize a single variant of the UNRES force field that … the backbone-local
and backbone-electrostatic interaction in … The most viable contributions to the “bulk” backbone-…
and backbone-electrostatic interaction in … The most viable contributions to the “bulk” backbone-…
Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies
NH Rogoża, MA Krupa, P Krupa, AK Sieradzan - Molecules, 2024 - mdpi.com
… multibody terms accounting for the coupling of the backbone–local and backbone–electrostatic …
field, the energy function is based on PMF, which contains an entropy contribution from …
field, the energy function is based on PMF, which contains an entropy contribution from …
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
A Antoniak, I Biskupek, KK Bojarski… - Journal of Molecular …, 2021 - Elsevier
… easy to parameterize. In particular, the site-site interaction potentials of most coarse-grained …
force field contains explicit terms that couple the backbone-local and backbone-electrostatic …
force field contains explicit terms that couple the backbone-local and backbone-electrostatic …
Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
… multibody terms that account for the coupling of the backbone-… correlation of the
backbone-electrostatic and backbone-local … -zero contributions to the penalty function are not …
backbone-electrostatic and backbone-local … -zero contributions to the penalty function are not …
[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
… In this paper, we contribute … electrostatic-interaction potentials of united peptide groups. U
c o r r ( 3 ) and U t u r n ( 3 ) are multibody terms that account for the coupling of the backbone-…
c o r r ( 3 ) and U t u r n ( 3 ) are multibody terms that account for the coupling of the backbone-…
Theory and practice of coarse-grained molecular dynamics of biologically important systems
… freedom contribute to … backbone-local and backbone-electrostatic conformational states,
which prevent overly compact local chain fragments [80]. Another way of including the multibody …
which prevent overly compact local chain fragments [80]. Another way of including the multibody …
Long-time dynamics of selected molecular-motor components using a physics-based coarse-grained approach
… the multibody or correlation terms that couple the backbone–local and backbone–electrostatic …
Two factors are likely to contribute to this different behavior. The 4YY2 system, although it …
Two factors are likely to contribute to this different behavior. The 4YY2 system, although it …