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 …
Protein folds vs. protein folding: Differing questions, different challenges
Protein fold prediction using deep-learning artificial intelligence (AI) has transformed the
field of protein structure prediction (1–3). By combining physical and geometric constraints …
field of protein structure prediction (1–3). By combining physical and geometric constraints …
From system modeling to system analysis: The impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules
The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …
fields, enables researchers to investigate biological systems at the molecular level with …
Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
AK Sieradzan, J Sans‐Duñó… - Journal of …, 2023 - Wiley Online Library
We report major algorithmic improvements of the UNRES package for physics‐based coarse‐
grained simulations of proteins. These include (i) introduction of interaction lists to optimize …
grained simulations of proteins. These include (i) introduction of interaction lists to optimize …
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 …
Multiscale modelling of biopolymers
This review overviews common biopolymer modelling approaches ranging from chemically
specific to highly coarse-grained techniques, along with their application ranges, strengths …
specific to highly coarse-grained techniques, along with their application ranges, strengths …
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 …
[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
Abstract Graphical Processor Units (GPUs) are nowadays widely used in all-atom molecular
simulations because of the advantage of efficient partitioning of atom pairs between the …
simulations because of the advantage of efficient partitioning of atom pairs between the …
A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules
A mapping of a macromolecule is a prescription to construct a simplified representation of
the system in which only a subset of its constituent atoms is retained. As the specific choice …
the system in which only a subset of its constituent atoms is retained. As the specific choice …
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 …
Intrinsically disordered proteins (IDPs) pose challenges to conventional experimental
techniques due to their large-scale conformational fluctuations and transient structural …
techniques due to their large-scale conformational fluctuations and transient structural …