The molecular basis for cellular function of intrinsically disordered protein regions
Intrinsically disordered protein regions exist in a collection of dynamic interconverting
conformations that lack a stable 3D structure. These regions are structurally heterogeneous …
conformations that lack a stable 3D structure. These regions are structurally heterogeneous …
Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution
Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …
OPLS3: a force field providing broad coverage of drug-like small molecules and proteins
The parametrization and validation of the OPLS3 force field for small molecules and proteins
are reported. Enhancements with respect to the previous version (OPLS2. 1) include the …
are reported. Enhancements with respect to the previous version (OPLS2. 1) include the …
Principles of protein structural ensemble determination
Highlights•The principles of protein structural ensemble determination are described.•The
use of experimental data averaged over multiple states is analysed.•Approaches for …
use of experimental data averaged over multiple states is analysed.•Approaches for …
Molecular dynamics simulations of intrinsically disordered proteins: force field evaluation and comparison with experiment
J Henriques, C Cragnell, M Skepo - Journal of chemical theory …, 2015 - ACS Publications
An increasing number of studies using molecular dynamics (MD) simulations of unfolded
and intrinsically disordered proteins (IDPs) suggest that current force fields sample …
and intrinsically disordered proteins (IDPs) suggest that current force fields sample …
Principles and overview of sampling methods for modeling macromolecular structure and dynamics
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …
Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a
high level of structural heterogeneity and are best described by ensembles consisting of …
high level of structural heterogeneity and are best described by ensembles consisting of …
Crowding in cellular environments at an atomistic level from computer simulations
The effects of crowding in biological environments on biomolecular structure, dynamics, and
function remain not well understood. Computer simulations of atomistic models of …
function remain not well understood. Computer simulations of atomistic models of …
SOURSOP: A Python package for the analysis of simulations of intrinsically disordered proteins
Conformational heterogeneity is a defining hallmark of intrinsically disordered proteins and
protein regions (IDRs). The functions of IDRs and the emergent cellular phenotypes they …
protein regions (IDRs). The functions of IDRs and the emergent cellular phenotypes they …