Modeling the structure, dynamics, and transformations of proteins with the UNRES force field

AK Sieradzan, C Czaplewski, P Krupa… - Protein folding: Methods …, 2022 - Springer
… 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

Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers

A Liwo, C Czaplewski, AK Sieradzan… - Progress in Molecular …, 2020 - Elsevier
… 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. …

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…

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-…

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 backboneelectrostatic
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

Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions

R Ślusarz, EA Lubecka, C Czaplewski… - Frontiers in Molecular …, 2022 - frontiersin.org
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 …

[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 contributeelectrostatic-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-…

Theory and practice of coarse-grained molecular dynamics of biologically important systems

A Liwo, C Czaplewski, AK Sieradzan, AG Lipska… - Biomolecules, 2021 - mdpi.com
… freedom contribute to … backbone-local and backbone-electrostatic conformational states,
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

A Liwo, M Pyrka, C Czaplewski, X Peng, AJ Niemi - Biomolecules, 2023 - mdpi.com
… the multibody or correlation terms that couple the backbone–local and backboneelectrostatic
Two factors are likely to contribute to this different behavior. The 4YY2 system, although it …