“…Two PPARγ-LBD crystal structures were retrieved from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein DataBank ( http://www.rcsb.org ): an active form with binding to the full agonist rosiglitazone and coactivator peptide [entry code: 1FM6 (Gampe et al, 2000 ); defined herein as PPAR–full], and an active form with binding to the partial agonist (2S)-2-(biphenyl-4-yloxy)-3-phenylpropanoic acid (LRG) [entry code: 3B3K (Montanari et al, 2008 ); defined herein as PPAR–partial]. The coordinates for IP (accession number: NP_004387.1 ) were built with the MODELER module, with bovine rhodopsin (entry code: 1HZX; Teller et al, 2001 ) as a template (Stitham et al, 2003 ; Accelrys, 2011 ; Li et al, 2016 ; Xu et al, 2016 ). According to previously published protocols (Stitham et al, 2003 ; Pérez-Villa et al, 2015 ), each protein structure was first equilibrated by 100 ns explicit solvent molecular dynamics simulation using the GROMACS4.6.7 program (Pronk et al, 2013 ) and CHARMM27 force field (Brooks et al, 2009 ).…”