Steered molecular dynamics simulation in rational drug design

PC Do, EH Lee, L Le - Journal of Chemical Information and …, 2018 - ACS Publications
Conventional de novo drug design is time consuming, laborious, and resource intensive. In
recent years, emerging in silico approaches have been proven to be critical to accelerate the …

Thyroid hormone receptor localization in target tissues

CS Anyetei-Anum, VR Roggero… - Journal of …, 2018 - joe.bioscientifica.com
The thyroid hormone receptors, TRα1, TRβ1 and other subtypes, are members of the
nuclear receptor superfamily that mediate the action of thyroid hormone signaling in …

PACKMOL: A package for building initial configurations for molecular dynamics simulations

L Martínez, R Andrade, EG Birgin… - Journal of …, 2009 - Wiley Online Library
Adequate initial configurations for molecular dynamics simulations consist of arrangements
of molecules distributed in space in such a way to approximately represent the system's …

TSH and thyrotropic agonists: key actors in thyroid homeostasis

JW Dietrich, G Landgrafe… - Journal of thyroid …, 2012 - Wiley Online Library
This paper provides the reader with an overview of our current knowledge of hypothalamic‐
pituitary‐thyroid feedback from a cybernetic standpoint. Over the past decades we have …

Single-molecule pulling simulations can discern active from inactive enzyme inhibitors

F Colizzi, R Perozzo, L Scapozza… - Journal of the …, 2010 - ACS Publications
Understanding ligand− protein recognition and interaction processes is of primary
importance for structure-based drug design. Traditionally, several approaches combining …

[HTML][HTML] Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: a new mode of ligand recognition and receptor stabilization

A Bernardes, PCT Souza, JRC Muniz, CG Ricci… - Journal of molecular …, 2013 - Elsevier
Peroxisome proliferator-activated receptors (PPARs) are members of a superfamily of
nuclear transcription factors. They are involved in mediating numerous physiological effects …

Nuclear receptor full-length architectures: confronting myth and illusion with high resolution

F Rastinejad, V Ollendorff, I Polikarpov - Trends in biochemical sciences, 2015 - cell.com
The crystal structures of three nuclear receptor (NR) complexes have emerged to reveal
their multidomain architectures on DNA. These pictures provide unprecedented views of …

Conformational dynamics of the estrogen receptor α: molecular dynamics simulations of the influence of binding site structure on protein dynamics

L Celik, JDD Lund, B Schiøtt - Biochemistry, 2007 - ACS Publications
We present 158 ns of unrestrained all-atom molecular dynamics (MD) simulations of the
human estrogen receptor α ligand binding domain (ERα LBD) sampling the conformational …

Gaining ligand selectivity in thyroid hormone receptors via entropy

L Martínez, AS Nascimento… - Proceedings of the …, 2009 - National Acad Sciences
Nuclear receptors are important targets for pharmaceuticals, but similarities between family
members cause difficulties in obtaining highly selective compounds. Synthetic ligands that …

Early-life glucocorticoids programme behaviour and metabolism in adulthood in zebrafish

KS Wilson, CS Tucker, EAS Al-Dujaili… - Journal of …, 2016 - joe.bioscientifica.com
Glucocorticoids (GCs) in utero influence embryonic development with consequent
programmed effects on adult physiology and pathophysiology and altered susceptibility to …