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 …
Advances in computational methods for ligand binding kinetics
Binding kinetic parameters can be correlated with drug efficacy, which in recent years led to
the development of various computational methods for predicting binding kinetic rates and …
the development of various computational methods for predicting binding kinetic rates and …
Recent progress in molecular simulation methods for drug binding kinetics
Highlights•Drug-target binding kinetics contribute to drug efficacy.•Many molecular dynamics
approaches to studying binding kinetics have been reported.•High quality datasets enable …
approaches to studying binding kinetics have been reported.•High quality datasets enable …
Mechanistic understanding from molecular dynamics in pharmaceutical research 2: lipid membrane in drug design
We review the use of molecular dynamics (MD) simulation as a drug design tool in the
context of the role that the lipid membrane can play in drug action, ie, the interaction …
context of the role that the lipid membrane can play in drug action, ie, the interaction …
[HTML][HTML] Fast approximative methods for study of ligand transport and rational design of improved enzymes for biotechnologies
O Vavra, J Damborsky, D Bednar - Biotechnology Advances, 2022 - Elsevier
Acceleration of chemical reactions by the enzymes optimized using protein engineering
represents one of the key pillars of the contribution of biotechnology towards sustainability …
represents one of the key pillars of the contribution of biotechnology towards sustainability …
Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters
J Chen, W Wang, H Sun, W He - Mini Reviews in Medicinal …, 2024 - ingentaconnect.com
Rational predictions on binding kinetics parameters of drugs to targets play significant roles
in future drug designs. Full conformational samplings of targets are requisite for accurate …
in future drug designs. Full conformational samplings of targets are requisite for accurate …
Molecular mechanics studies of factors affecting overall rate in cascade reactions: Multi‐enzyme colocalization and environment
Millions of years of evolution have optimized many biosynthetic pathways by use of multi‐
step catalysis. In addition, multi‐step metabolic pathways are commonly found in and on …
step catalysis. In addition, multi‐step metabolic pathways are commonly found in and on …
Contact map fingerprints of protein–ligand unbinding trajectories reveal mechanisms determining residence times computed from scaled molecular dynamics
The binding kinetic properties of potential drugs may significantly influence their subsequent
clinical efficacy. Predictions of these properties based on computer simulations provide a …
clinical efficacy. Predictions of these properties based on computer simulations provide a …
Bell-Evans model and steered molecular dynamics in uncovering the dissociation kinetics of ligands targeting G-protein-coupled receptors
Recently, academic and industrial scientific communities involved in kinetics-based drug
development have become immensely interested in predicting the drug target residence …
development have become immensely interested in predicting the drug target residence …
Combining hypothesis-and data-driven neuroscience modeling in FAIR workflows
Modeling in neuroscience occurs at the intersection of different points of view and
approaches. Typically, hypothesis-driven modeling brings a question into focus so that a …
approaches. Typically, hypothesis-driven modeling brings a question into focus so that a …