Computational protein structure refinement: almost there, yet still so far to go
M Feig - Wiley Interdisciplinary Reviews: Computational …, 2017 - Wiley Online Library
Protein structures are essential in modern biology yet experimental methods are far from
being able to catch up with the rapid increase in available genomic data. Computational …
being able to catch up with the rapid increase in available genomic data. Computational …
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 …
Experimental accuracy in protein structure refinement via molecular dynamics simulations
Refinement is the last step in protein structure prediction pipelines to convert approximate
homology models to experimental accuracy. Protocols based on molecular dynamics (MD) …
homology models to experimental accuracy. Protocols based on molecular dynamics (MD) …
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
C Czaplewski, A Karczyńska… - Nucleic Acids …, 2018 - academic.oup.com
A server implementation of the UNRES package (http://www. unres. pl) for coarse-grained
simulations of protein structures with the physics-based UNRES model, coined a name …
simulations of protein structures with the physics-based UNRES model, coined a name …
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale …
The general theory of the construction of scale-consistent energy terms in the coarse-
grained force fields presented in Paper I of this series has been applied to the revision of the …
grained force fields presented in Paper I of this series has been applied to the revision of the …
Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours
An ongoing challenge in protein chemistry is to identify the underlying interaction energies
that capture protein dynamics. The traditional trade-off in biomolecular simulation between …
that capture protein dynamics. The traditional trade-off in biomolecular simulation between …
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 …
Structure and physicochemical properties of the Aβ42 tetramer: multiscale molecular dynamics simulations
Despite years of intensive research, little is known about oligomeric structures present
during Alzheimer's disease (AD). Excess of amyloid beta (Aβ) peptides and their …
during Alzheimer's disease (AD). Excess of amyloid beta (Aβ) peptides and their …
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 …