[HTML][HTML] Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Emerging computational methods for the rational discovery of allosteric drugs

JR Wagner, CT Lee, JD Durrant, RD Malmstrom… - Chemical …, 2016 - ACS Publications
Allosteric drug development holds promise for delivering medicines that are more selective
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …

Common activation mechanism of class A GPCRs

Q Zhou, D Yang, M Wu, Y Guo, W Guo, L Zhong, X Cai… - Elife, 2019 - elifesciences.org
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human
physiology. Understanding receptor activation mechanism is critical for discovering novel …

Gaussian accelerated molecular dynamics: unconstrained enhanced sampling and free energy calculation

Y Miao, VA Feher, JA McCammon - Journal of chemical theory …, 2015 - ACS Publications
A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

Activation and allosteric modulation of a muscarinic acetylcholine receptor

AC Kruse, AM Ring, A Manglik, J Hu, K Hu, K Eitel… - Nature, 2013 - nature.com
Despite recent advances in crystallography and the availability of G-protein-coupled
receptor (GPCR) structures, little is known about the mechanism of their activation process …

Improved reweighting of accelerated molecular dynamics simulations for free energy calculation

Y Miao, W Sinko, L Pierce, D Bucher… - Journal of chemical …, 2014 - ACS Publications
Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of
conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they …

[HTML][HTML] Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy

D Ni, J Wei, X He, AU Rehman, X Li, Y Qiu, J Pu… - Chemical …, 2021 - pubs.rsc.org
Allostery, which is one of the most direct and efficient methods to fine-tune protein functions,
has gained increasing recognition in drug discovery. However, there are several challenges …

[HTML][HTML] Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular …

MCR Melo, RC Bernardi… - The Journal of …, 2020 - pubs.aip.org
Molecular interactions are essential for regulation of cellular processes from the formation of
multi-protein complexes to the allosteric activation of enzymes. Identifying the essential …

[HTML][HTML] Structural basis of efficacy-driven ligand selectivity at GPCRs

AS Powers, V Pham, WAC Burger, G Thompson… - Nature Chemical …, 2023 - nature.com
A drug's selectivity for target receptors is essential to its therapeutic utility, but achieving
selectivity between similar receptors is challenging. The serendipitous discovery of ligands …

[PDF][PDF] Molecular insights into the biased signaling mechanism of the μ-opioid receptor

X Cong, D Maurel, H Déméné, I Vasiliauskaité-Brooks… - Molecular Cell, 2021 - cell.com
GPCR functional selectivity opens new opportunities for the design of safer drugs. Ligands
orchestrate GPCR signaling cascades by modulating the receptor conformational …