Chemogenomic profiling of human and microbial FK506-binding proteins
S Pomplun, C Sippel, A Hähle, D Tay… - Journal of medicinal …, 2018 - ACS Publications
FK506-binding proteins (FKBPs) are evolutionarily conserved proteins that display peptidyl-
prolyl isomerase activities and act as coreceptors for immunosuppressants. Microbial …
prolyl isomerase activities and act as coreceptors for immunosuppressants. Microbial …
Conformational transitions and convergence of absolute binding free energy calculations
M Lapelosa, E Gallicchio, RM Levy - Journal of Chemical Theory …, 2012 - ACS Publications
The Binding energy distribution analysis method (BEDAM) is employed to compute the
standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) …
standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) …
II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands
The recently proposed fast switching double annihilation (FS-DAM)[Cardelli et al., J. Chem.
Theory Comput., 2015, 11, 423] is aimed at computing the absolute standard dissociation …
Theory Comput., 2015, 11, 423] is aimed at computing the absolute standard dissociation …
The precise chemical–physical nature of the pharmacore in FK506 binding protein inhibition: eltex, a new class of nanomolar FKBP12 ligands
MR Martina, E Tenori, M Bizzarri… - Journal of Medicinal …, 2013 - ACS Publications
Due to its central role in immunosuppression and cell proliferation and due to its specific
peptidyl-prolyl-isomerase (PPI) function, the FKBP protein family is at the crossroad of …
peptidyl-prolyl-isomerase (PPI) function, the FKBP protein family is at the crossroad of …
Multiple Bennett acceptance ratio made easy for replica exchange simulations
P Procacci - The Journal of Chemical Physics, 2013 - pubs.aip.org
In this paper, we illustrate a practical technique to improve the efficiency of the so-called
multiple Bennett acceptance ratio (MBAR) estimator [Shirts and Chodera, J. Chem. Phys …
multiple Bennett acceptance ratio (MBAR) estimator [Shirts and Chodera, J. Chem. Phys …
Electronic circular dichroism and nuclear magnetic resonance studies of peptides derived from the FKBP52‐interacting β‐turn of the hERα ligand‐binding domain
C Byrne, M Belnou, EE Baulieu, O Lequin… - Peptide …, 2019 - Wiley Online Library
When located at the surface of proteins, turns containing a Pro‐Gly (PG) motif are often
involved in protein/protein interactions and may participate in intracellular signaling …
involved in protein/protein interactions and may participate in intracellular signaling …
[HTML][HTML] Role of ligand reorganization and conformational restraints on the binding free energies of DAPY non-nucleoside inhibitors to HIV reverse transcriptase
E Gallicchio - Computational molecular bioscience, 2012 - ncbi.nlm.nih.gov
The results of computer simulations of the binding of etravirine (TMC125) and rilpivirine
(TMC278) to HIV reverse transcriptase are reported. It is confirmed that consistent binding …
(TMC278) to HIV reverse transcriptase are reported. It is confirmed that consistent binding …
A β-turn motif in the steroid hormone receptor's ligand-binding domains interacts with the peptidyl-prolyl isomerase (PPIase) catalytic site of the immunophilin FKBP52
C Byrne, MA Henen, M Belnou, FX Cantrelle… - Biochemistry, 2016 - ACS Publications
The immunophilin FKBP52 interacts with nuclear steroid hormone receptors. Studying the
crystal structure of human estrogen receptor α (hERα) and using nuclear magnetic …
crystal structure of human estrogen receptor α (hERα) and using nuclear magnetic …
Reformulating the entropic contribution in molecular docking scoring functions
P Procacci - Journal of Computational Chemistry, 2016 - Wiley Online Library
We have derived, in the context of the Rigid Rotor Harmonic Approximation (RRHO), a
general mass and Planck's constant h independent expression for the dissociation free …
general mass and Planck's constant h independent expression for the dissociation free …
Energy-driven undocking (edu-hrem) in solute tempering replica exchange simulations
P Procacci, M Bizzarri, S Marsili - Journal of Chemical Theory and …, 2014 - ACS Publications
We present a new computational strategy for calculating the absolute binding free energy for
protein ligand association in the context of atomistic simulation in explicit solvent. The …
protein ligand association in the context of atomistic simulation in explicit solvent. The …