AutoDock Vina is arguably one of the fastest and most widely used open-source programs
for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks …

Allosteric regulation plays an important role in many biological processes, such as signal
transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental …

Molecular docking has been successfully used in computer-aided molecular design projects
for the identification of ligand poses within protein binding sites. However, relying on …

Prediction categories in the Critical Assessment of Structure Prediction (CASP) experiments
change with the need to address specific problems in structure modeling. In CASP15, four …

The vitamin D receptor (VDR), an endocrine nuclear receptor for 1α,25-dihydroxyvitamin D3,
acts also as a bile acid sensor by binding lithocholic acid (LCA). The crystal structure of the …

CASP15 introduced a new category, ligand prediction, where participants were provided
with a protein or nucleic acid sequence, SMILES line notation, and stoichiometry for ligands …

Activity-based protein profiling (ABPP) has been used extensively to discover and optimize
selective inhibitors of enzymes. Here, we show that ABPP can also be implemented to …

Pioglitazone (Pio) is a Food and Drug Administration-approved drug for type-2 diabetes that
binds and activates the nuclear receptor peroxisome proliferator-activated receptor γ (…

In this paper we describe our approaches to predict the binding mode of twenty BACE1
ligands as part of Grand Challenge 4 (GC4), organized by the Drug Design Data Resource. …

The retinoic X receptor (RXR) plays a crucial role in the superfamily of nuclear receptors (NRs)
by acting as an obligatory partner of several nuclear receptors; its role as a transcription …