Perspective: Advances, challenges, and insight for predictive coarse-grained models
WG Noid - The Journal of Physical Chemistry B, 2023 - ACS Publications
By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …
computational and conceptual advantages for studying soft materials. In particular, bottom …
How to learn from inconsistencies: Integrating molecular simulations with experimental data
Molecular simulations and biophysical experiments can be used to provide independent
and complementary insights into the molecular origin of biological processes. A particularly …
and complementary insights into the molecular origin of biological processes. A particularly …
[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization
ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …
role in all DNA-templated processes, including gene transcription, gene regulation, and …
[HTML][HTML] Predicting chemical shifts with graph neural networks
Inferring molecular structure from Nuclear Magnetic Resonance (NMR) measurements
requires an accurate forward model that can predict chemical shifts from 3D structure …
requires an accurate forward model that can predict chemical shifts from 3D structure …
Consistent force field captures homologue-resolved HP1 phase separation
Many proteins have been shown to function via liquid–liquid phase separation.
Computational modeling could offer much needed structural details of protein condensates …
Computational modeling could offer much needed structural details of protein condensates …
Active learning of the conformational ensemble of proteins using maximum entropy VAMPNets
DE Kleiman, D Shukla - Journal of Chemical Theory and …, 2023 - ACS Publications
Rapid computational exploration of the free energy landscape of biological molecules
remains an active area of research due to the difficulty of sampling rare state transitions in …
remains an active area of research due to the difficulty of sampling rare state transitions in …
Unifying coarse-grained force fields for folded and disordered proteins
Liquid–liquid phase separation drives the formation of biological condensates that play
essential roles in transcriptional regulation and signal sensing. Computational modeling …
essential roles in transcriptional regulation and signal sensing. Computational modeling …
Integrating cryo-EM and NMR data
JA Geraets, KR Pothula, GF Schröder - Current opinion in structural biology, 2020 - Elsevier
Single-particle cryo-electron microscopy (cryo-EM) is increasingly used as a technique to
determine the atomic structure of challenging biological systems. Recent advances in …
determine the atomic structure of challenging biological systems. Recent advances in …
Method for accurately predicting solvation structure
Accurately predicting the molecular structure of solutions is a fundamental scientific
challenge. Using quantum mechanical density functional theory (DFT) to make these …
challenge. Using quantum mechanical density functional theory (DFT) to make these …
Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water
Experiment directed simulation (EDS) is a method within a class of techniques seeking to
improve molecular simulations by minimally biasing the system Hamiltonian to reproduce …
improve molecular simulations by minimally biasing the system Hamiltonian to reproduce …