Molecular dynamics docking driven by NMR-derived restraints to determine the structure of the calicheamicin 纬11 oligosaccharide domain complexed to duplex DNA - Smith, Gomez-Paloma, et al. - 1996 () Citation Co
In this case, VS protocols that combine ligand-based approaches (a fast, although less accurate, step to prefilter hits from very large databases of compounds) with receptor-based techniques (a more accurate step to evaluate selected hits by using docking and/or molecular dynamics free energy ...
www.nature.com/scientificreports OPEN received: 05 July 2016 accepted: 20 September 2016 Published: 10 October 2016 Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies Miguel A. Soler1, Ario de Marco2 & Sara ...
Unlike docking simulation, molecular dynamics considers the solvent effects, sampling conformation, and clustering of the receptor, which could account for the conformational dynamics of the protein. Hence, an investigator could evaluate better the stability of a drug candidate in the binding pocket of...
It includes a range of tools for molecular docking, virtual screening, protein modeling, and analysis of molecular dynamics simulations. The molecular docking component is used to predict the binding mode of a ligand (small molecule) to a target protein and to estimate the strength of the ...
The control ligand had an XP docking of − 9.5 kcal/mol and an MM-GBSA value of − 8.4 kcal/mol. To gain more comprehensive insights into the binding dynamics of the PknG-cyclo-(L-Pro-4-OH-L-Leu) and Pks13-vazabitide A complexes, MD simulations and post-MD-ΔGbind simulations...
docking to structural ensembles generated by molecular dynamics (MD) simulations. Does the incorporation of multiple receptor conformations allow pushing the borders for molecular docking or does it just lead to an artificial increase in false positive hit rates due to a broader conformational space of...
A new method for flexible docking by multicanonical molecular dynamics simulation is presented. The method was applied to the binding of a short proline-rich peptide to a Src homology 3 (SH3) domain. The peptide and the side-chains at the ligand binding cleft of SH3 were completely flexible...
Molecular dynamics SARS-CoV-2 HIV protease inhibitors Molecular docking COVID-19 1. Introduction Human coronavirus (HCoV) strains, SARS-CoV-1 (2003), MERS-Cov (2012) as well as the newly emerged SARS-CoV-2 (2019), are responsible for respiratory syndromes that can cause serious infections re...
Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure. At an optimal temperature, MP-4 achieves maximal binding while above and below the optimum temperature, its functional activity is hampered due to ...