Advanced sampling methods for multiscale simulation of disordered proteins and dynamic interactions
Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in
biology and human diseases. It is now also recognized that many IDPs remain dynamic …
biology and human diseases. It is now also recognized that many IDPs remain dynamic …
Efficient sampling of high-dimensional free-energy landscapes with parallel bias metadynamics
J Pfaendtner, M Bonomi - Journal of chemical theory and …, 2015 - ACS Publications
Metadynamics accelerates sampling of molecular dynamics while reconstructing
thermodynamic properties of selected descriptors of the system. Its main practical difficulty …
thermodynamic properties of selected descriptors of the system. Its main practical difficulty …
Replica-exchange umbrella sampling combined with Gaussian accelerated molecular dynamics for free-energy calculation of biomolecules
We have developed an enhanced conformational sampling method combining replica-
exchange umbrella sampling (REUS) with Gaussian accelerated molecular dynamics …
exchange umbrella sampling (REUS) with Gaussian accelerated molecular dynamics …
Exploring high‐dimensional free energy landscapes of chemical reactions
Molecular dynamics (MD) techniques are widely used in computing free energy changes for
conformational transitions and chemical reactions, mainly in condensed matter systems …
conformational transitions and chemical reactions, mainly in condensed matter systems …
Replica-exchange methods for biomolecular simulations
In this study, a replica-exchange method was developed to overcome conformational
sampling difficulties in computer simulations of spin glass or other systems with rugged free …
sampling difficulties in computer simulations of spin glass or other systems with rugged free …
Binding kinetics study of SARS-CoV-2 main protease and potential inhibitors via molecular dynamics simulations
The pandemic COVID-19 was induced by the novel coronavirus SARS-CoV-2. The virus
main protease (Mpro) cleaves the coronavirus polyprotein translated from the viral RNA in …
main protease (Mpro) cleaves the coronavirus polyprotein translated from the viral RNA in …
Boosting the conformational sampling by combining replica exchange with solute tempering and well‐sliced metadynamics
AB Kapakayala, NN Nair - Journal of Computational Chemistry, 2021 - Wiley Online Library
Methods that combine collective variable (CV) based enhanced sampling and global
tempering approaches are used in speeding‐up the conformational sampling and free …
tempering approaches are used in speeding‐up the conformational sampling and free …
Phase space and collective variable based simulation methods for studies of rare events
In this work, we review molecular simulation methods for studies of rare events. Specifically
highlighted are recent advances and biological applications of methods that utilise unbiased …
highlighted are recent advances and biological applications of methods that utilise unbiased …
Enhanced conformational sampling of N-glycans in solution with replica state exchange metadynamics
Molecular dynamics (MD) simulation of a N-glycan in solution is challenging because of
high-energy barriers of the glycosidic linkages, functional group rotational barriers, and …
high-energy barriers of the glycosidic linkages, functional group rotational barriers, and …
A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus
Argonaute proteins (Ago) are core components of the RNA Induced Silencing Complex
(RISC) that load and utilize small guide nucleic acids to silence mRNAs or cleave foreign …
(RISC) that load and utilize small guide nucleic acids to silence mRNAs or cleave foreign …