Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
Theory and practice of coarse-grained molecular dynamics of biologically important systems
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate
biomolecular systems at large time and size scales, compared to those accessible to all …
biomolecular systems at large time and size scales, compared to those accessible to all …
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
Abstract The UNited RESidue (UNRES) force field was tested in the 14th Community Wide
Experiment on the Critical Assessment of Techniques for Protein Structure Prediction …
Experiment on the Critical Assessment of Techniques for Protein Structure Prediction …
Insight into the initial stages of the folding process in onconase revealed by UNRES
The unfolded state of proteins presents many challenges to elucidate the structural basis for
biological function. This state is characterized by a large degree of structural heterogeneity …
biological function. This state is characterized by a large degree of structural heterogeneity …
Modeling the structure, dynamics, and transformations of proteins with the UNRES force field
The physics-based united-residue (UNRES) model of proteins (www. unres. pl) has been
designed to carry out large-scale simulations of protein folding. The force field has been …
designed to carry out large-scale simulations of protein folding. The force field has been …
Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2)
I Biskupek, A Gieldon - International Journal of Molecular Sciences, 2024 - mdpi.com
The SARS-CoV-2 virus, commonly known as COVID-19, occurred in 2019. It is a highly
contagious illness with effects ranging from mild symptoms to severe illness. It is also one of …
contagious illness with effects ranging from mild symptoms to severe illness. It is also one of …
Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web Server
Intrinsically disordered proteins (IDPs) contain more charged amino acids than folded
proteins, resulting in a lack of hydrophobic core (s) and a tendency to adopt rapidly …
proteins, resulting in a lack of hydrophobic core (s) and a tendency to adopt rapidly …
Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery
C Sikorska, A Liwo - The Journal of Physical Chemistry B, 2022 - ACS Publications
By analyzing the Kubo-cluster-cumulant expansion of the potential of mean force of
polypeptide chains corresponding to backbone-local interactions averaged over the rotation …
polypeptide chains corresponding to backbone-local interactions averaged over the rotation …
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
Fullerenes, particularly C60, exhibit unique properties that make them promising candidates
for various applications, including drug delivery and nanomedicine. However, their …
for various applications, including drug delivery and nanomedicine. However, their …
Pseudopotentials for coarse‐grained cross‐link‐assisted modeling of protein structures
Pseudopotentials for the chemical cross‐links comprising the glutamic‐and aspartic‐acid
side chains bridged with adipic‐(ADH) or pimelic‐acid hydrazide (PDH), and the lysine side …
side chains bridged with adipic‐(ADH) or pimelic‐acid hydrazide (PDH), and the lysine side …