Molecular docking of C-A1 (in yellow) in HIV-1 hexameric capsid structure 4XFZ.pdb with bound PF-74 (in green) using the Compute: SiteFinder option in MOE software. A single C-A1 conformation is shown bound to capsid. The two subunits of capsid are depicted inbrownandturquoiserespectively...
Melatonin can also inhibit the activity of MMPs through binding of melatonin to the active site, as shown in molecular docking simulations [97]. As previously explained, melatonin can further suppress deleterious effects of excessive MMPs by directly scavenging the ROS that increase MMP expression as...
Exosomes could be involved in intercellular communication and in the pathogenesis of infectious and degenerative diseases. The molecular mechanisms of exosome biogenesis and secretion are, however, poorly understood. Using an RNA interference (RNAi) screen, we identified five Rab GTPases that promote ...
The extracellular M2-M3 region is located at the interface between the ECD and the TMDs and has been shown experimentally to be involved in channel gating (e.g., CamposCaro et al., 1996, Rovira et al., 1998, Grosman et al., 2000a). Mutations in this loop influence gating and ...
S.K.B was involved in all aspects of the work including single-molecule assay development performing experiments and data analysis. S.K.B. and M.J.L. designed the experiments and prepared the manuscript. S.S. expressed and purified the isolated domains and carried out the Biacore-binding stu...
CABYR is a polymorphic calcium-binding protein of the sperm fibrous sheath (FS) which gene contains two coding regions (CR-A and CR-B) and is tyrosine as well as serine/threonine phosphorylated during in vitro sperm capacitation. Thus far, the detailed information on CABYR protein expression ...
In this work, homology modeling, substrate docking and molecular dynamics simulations were carried out to learn more about the transition between the “outward-open” and “outward-open occluded” states. We identified a transition state involving the highly-conserved unwound TM6 region in which the...
This model suggested that the aspartic acid and isoleucine of the MEK6 activation loop sequence DSVAKTI might be involved in substrate binding. In the model, the isoleucine of the MEK6 activation loop is in the P+1 specificity pocket of the MAP3K when threonine is in the active site (Fig...
Ranked #1 onBlind Docking on PDBbind(Top-1 RMSD (Med.) metric) Get a GitHub badge TaskDatasetModelMetric NameMetric ValueGlobal RankResultBenchmark Blind DockingPDBbindEQUIBIND+GNINATop-1 RMSD (Med.)4.9# 1 Compare Blind DockingPDBbindP2RANK+SMINATop-1 RMSD (%<2)20.4# 2 ...
To do so, we map this manifold to the product space of the degrees of freedom (translational, rotational, and torsional) involved in docking and develop an efficient diffusion process on this space. Empirically,