Recent force field strategies for intrinsically disordered proteins

J Mu, H Liu, J Zhang, R Luo… - Journal of chemical …, 2021 - ACS Publications
Intrinsically disordered proteins (IDPs) are widely distributed across eukaryotic cells, playing
important roles in molecular recognition, molecular assembly, post-translational …

Rational drug design targeting intrinsically disordered proteins

H Wang, R **ong, L Lai - Wiley Interdisciplinary Reviews …, 2023 - Wiley Online Library
Intrinsically disordered proteins (IDPs) are proteins that perform important biological
functions without well‐defined structures under physiological conditions. IDPs can form …

EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction

J Zhao, A Blayney, X Liu, L Gandy, W **, L Yan… - Nature …, 2021 - nature.com
Epigallocatechin gallate (EGCG) from green tea can induce apoptosis in cancerous cells,
but the underlying molecular mechanisms remain poorly understood. Using SPR and NMR …

Toward accurate simulation of coupling between protein secondary structure and phase separation

Y Zhang, S Li, X Gong, J Chen - Journal of the American Chemical …, 2023 - ACS Publications
Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies
the formation of a biomolecular condensate. Together with theory and experiment, efficient …

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

UR Shrestha, JC Smith, L Petridis - Communications biology, 2021 - nature.com
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged
experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from …

Recent advances in atomic molecular dynamics simulation of intrinsically disordered proteins

W Wang - Physical Chemistry Chemical Physics, 2021 - pubs.rsc.org
Intrinsically disordered proteins (IDPs) play important roles in cellular functions. The inherent
structural heterogeneity of IDPs makes the high-resolution experimental characterization of …

Machine learning generation of dynamic protein conformational ensembles

LE Zheng, S Barethiya, E Nordquist, J Chen - Molecules, 2023 - mdpi.com
Machine learning has achieved remarkable success across a broad range of scientific and
engineering disciplines, particularly its use for predicting native protein structures from …

Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma

P Kulkarni, VBP Leite, S Roy, S Bhattacharyya… - Biophysics …, 2022 - pubs.aip.org
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they
are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as …

Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations

Y Zhang, X Liu, J Chen - Journal of chemical theory and …, 2023 - ACS Publications
Replica exchange with solute tempering (REST) is a highly effective variant of replica
exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling …

[HTML][HTML] Targeting intrinsically disordered proteins through dynamic interactions

J Chen, X Liu, J Chen - Biomolecules, 2020 - mdpi.com
Intrinsically disordered proteins (IDPs) are over-represented in major disease pathways and
have attracted significant interest in understanding if and how they may be targeted using …