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Structural Analysis of Peptide Fragments Following The Hydrolysis of Bovine Serum Albumin by Trypsin and Chymotrypsin
(Taylor & Francis Inc, 2016)
Peptide bond hydrolysis of bovine serum albumin (BSA) by chymotrypsin and trypsin was investigated by employing time-resolved fluorescence spectroscopy. As a fluorescent cross-linking reagent N-(1-pyrenyl) maleimide (PM) ...
Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets
(Frontiers Media, 2020)
Three allosteric glycolytic enzymes, phosphofructokinase, glyceraldehyde-3 phosphate dehydrogenase and pyruvate kinase, associated with bacterial, parasitic and human species, were explored to identify potential allosteric ...
Transmembrane helix 6 observed at the interface of beta(2)AR homodimers in blind docking studies
(Taylor & Francis Inc, 2015)
Peptide- and protein-protein dockings were carried out on beta(2)-adrenergic receptor (beta(2)AR) to confirm the presence of transmembrane helix 6 (TM6) at the interface region between two beta(2)AR monomers thereby its ...
A Docking Study Using Atomistic Conformers Generated via Elastic Network Model for Cyclosporin A/Cyclophilin A Complex
(Taylor & Francis Inc, 2009)
Anisotropic network model is used to generate a set of distinct conformations for cylophilin A (CypA). The native structure is deformed to different extents along each of the lowest-frequency modes (first 7 modes) both in ...
Assessing protein-ligand binding modes with computational tools: the case of PDE4B
(Springer, 2017)
In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects we present a protocol to rank newly designed molecules through the estimation of their IC values. Our ...
Investigation of Allosteric Coupling in Human Beta(2)-Adrenergic Receptor in the Presence of Intracellular Loop 3
(BMC, 2016)
Background: This study investigates the allosteric coupling that exists between the intra- and extracellular parts of human beta(2)-adrenergic receptor (beta(2)-AR) in the presence of the intracellular loop 3 (ICL3) which ...
Molecular docking study based on pharmacophore modeling for novel PhosphodiesteraseIV ınhibitors
(Wiley-VCH Verlag GmbH, 2012)
In this study pharmacophore modelling was carried out for novel PhosphodiesteraseIV (PDEIV) inhibitors. A pharmacophore-based virtual screening which resulted in 1959 hit compounds was performed with six chemical databases. ...
Potential allosteric sites captured in glycolytic enzymes via residue-based network models: Phosphofructokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase
(Elsevier, 2022)
Likelihood of new allosteric sites for glycolytic enzymes, phosphofructokinase (PFK), glyceraldehyde-3phosphate dehydrogenase (GADPH) and pyruvate kinase (PK) was evaluated for bacterial, parasitic and human species. ...
Drug repositioning to propose alternative modulators for glucocorticoid receptor through structure-based virtual screening
(Taylor & Francis Inc, 2022)
Drug repositioning has recently become one of the widely used drug design approaches in proposing alternative compounds with potentially fewer side effects. In this study, structure-based pharmacophore modelling and docking ...
Effect of intracellular loop 3 on intrinsic dynamics of human 2-adrenergic receptor
(Bmc, 2013)
Background: To understand the effect of the long intracellular loop 3 (ICL3) on the intrinsic dynamics of human beta(2)-adrenergic receptor, molecular dynamics (MD) simulations were performed on two different models, both ...