Enhanced sampling methods for molecular dynamics simulations
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …
molecular dynamics simulations and allow the sampling of larger portions of the …
Protein design: From the aspect of water solubility and stability
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …
sequence and 3D-conformation. Their manipulation represents important aspects of the …
[HTML][HTML] Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations
Antibodies elicited by infection accumulate somatic mutations in germinal centers that can
increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related …
increase affinity for cognate antigens. We analyzed 6 independent groups of clonally related …
Molecular dynamics simulations in drug discovery and pharmaceutical development
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …
development process. In this review, we give a broad overview of the current application …
Molecular orientation-dependent energetic shifts in solution-processed non-fullerene acceptors and their impact on organic photovoltaic performance
The non-fullerene acceptors (NFAs) employed in state-of-art organic photovoltaics (OPVs)
often exhibit strong quadrupole moments which can strongly impact on material energetics …
often exhibit strong quadrupole moments which can strongly impact on material energetics …
Using metadynamics to explore complex free-energy landscapes
Metadynamics is an atomistic simulation technique that allows, within the same framework,
acceleration of rare events and estimation of the free energy of complex molecular systems …
acceleration of rare events and estimation of the free energy of complex molecular systems …
Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP …
X-linked inhibitor of apoptosis protein (XIAP) is a member of inhibitor of apoptosis protein
(IAP) family responsible for neutralizing the caspases-3, caspases-7, and caspases-9 …
(IAP) family responsible for neutralizing the caspases-3, caspases-7, and caspases-9 …
Molecular dynamics simulation for all
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …
has expanded dramatically in recent years. These simulations capture the behavior of …
[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …
generating pathways and rate constants for rare events such as protein folding and protein …
Dual synergistic inhibition of COX and LOX by potential chemicals from Indian daily spices investigated through detailed computational studies
Abstract Cyclooxygenase (COX) and Lipoxygenase (LOX) are essential enzymes for
arachidonic acid (AA) to eicosanoids conversion. These AA-derived eicosanoids are …
arachidonic acid (AA) to eicosanoids conversion. These AA-derived eicosanoids are …