We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in an...

N-heterocyclic carbenes (NHCs) represent a leading class of ligands in organometallic chemistry, but have been rarely exploited as stabilizers for metal nanoparticles (NPs). We report the first example of NHC stabilized Pd-NPs that demonstrate long term stability. These NHC Pd-NPs were synthesized by a facile ligand exchange protocol using rationally designed long chained NHCs (LC-NHCs). Furthe...

RESOLVE is a widely used program for statistical density modification, local pattern matching, automated model-building, automated ligand-fitting, and prime-and-switch minimum bias phasing (Terwilliger 2000, Terwilliger 2003). In recent years it has been developed primarily in the context of PHENIX, which is a rapidly growing software suite for the automated determination of macromolecular stru...

Previous studies have shown that the fraction of hormone or drug that is plasma protein bound is readily available for transport through the brain endothelial wall, i.e., the blood-brain barrier (BBB). To test whether these observations are reconcilable with the free-hormone hypothesis, a tracer-kinetic model is used in the present investigations to analyze in vivo initial extraction data on BB...

This study describes a form of partial agonism for a CD8+ CTL clone, S15, in which perforin-dependent killing and IFN-gamma production were lost but Fas (APO1 or CD95)-dependent cytotoxicity preserved. Cloned S15 CTL are H-2Kd restricted and specific for a photoreactive derivative of the Plasmodium berghei circumsporozoite peptide PbCS 252-260 (SYIPSAEKI). The presence of a photoactivatable gro...

Crystal structures can identify ligand-receptor interactions and assist the development of novel therapeutics, but experimental challenges sometimes necessitate the use of homologous proteins. Tropisetron is an orthosteric ligand at both 5-HT3 and α7 nACh receptors and its binding orientation has been determined in the structural homologue AChBP (pdbid: 2WNC). Co-crystallisation with a structur...

The specificity of carbohydrate-protein interactions can greatly outstrip that of many other ligand-binding systems; such is the enormous density of information that sugars can convey. In addition, macromolecules allow for the fine-tuning of active drug delivery through their great ability to undergo site-specific modification and their inherent physicochemical properties. Once combined, these ...