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 …
how macromolecules carry out their functions in the cell. Significant advances have been …
Emerging computational methods for the rational discovery of allosteric drugs
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 …
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …
Common activation mechanism of class A GPCRs
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human
physiology. Understanding receptor activation mechanism is critical for discovering novel …
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 …
sampling and free energy calculation of biomolecules is presented. By constructing a boost …
Activation and allosteric modulation of a muscarinic acetylcholine receptor
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 …
receptor (GPCR) structures, little is known about the mechanism of their activation process …
Improved reweighting of accelerated molecular dynamics simulations for free energy calculation
Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of
conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they …
conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they …
Structural basis of efficacy-driven ligand selectivity at GPCRs
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 …
selectivity between similar receptors is challenging. The serendipitous discovery of ligands …
Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy
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 …
has gained increasing recognition in drug discovery. However, there are several challenges …
Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics …
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 …
multi-protein complexes to the allosteric activation of enzymes. Identifying the essential …
Controlling allosteric networks in proteins
NV Dokholyan - Chemical reviews, 2016 - ACS Publications
Allosteric transition, defined as conformational changes induced by ligand binding, is one of
the fundamental properties of proteins. Allostery has been observed and characterized in …
the fundamental properties of proteins. Allostery has been observed and characterized in …