Precomputed affinity maps are used by AutoDock to efficiently describe rigid biomolecules called receptors in automated docking. These maps greatly speed up the docking process and allow users to experiment with the forcefield. Here, we present AutoGridFR (AGFR): a software tool facilitating the calculation of these maps. We describe a new version of the AutoSite algorithm that improves the description of binding pockets automatically detected on receptors, and an algorithm for adding affinity gradients which help search methods optimize solution using fewer evaluations of the scoring functions. AGFR supports the calculation of maps for various advanced docking techniques such as covalent docking, hydrated docking, and docking with flexible receptor sidechains. Maps are stored in a single file along with metadata supporting data provenance, reproducibility, and facilitating their management. Finally, maps can be calculated from the command line or through a modern graphical user interface which also supports their visualization. © 2019 Wiley Periodicals, Inc.

No abstract

No abstract

<p>Newborns with critical coarctation of the aorta with a closed arterial duct often require surgical repair. Primary repair is associated with a high risk of unfavorable outcomes owing to severe systemic outflow obstruction and multiple organ failure. We present the case of a premature male newborn (weight = 1.9 kg) with critical coarctation of the aorta and multiple organ dysfunction syndrome with a closed arterial duct who successfully underwent isthmus stenting as a palliative step before surgical repair. The indication for primary stent implantation was decompensated metabolic acidosis. For stenting, the retroperitoneal approach was selected, and elective surgical cut-down of the right iliac artery was performed. Standard coronary stents (diameter = 4 mm; length = 13 mm) were delivered via a 4F sheath. The right iliac artery was repaired after sheath removal. The procedure was successful, and there were no procedural complications. Four days after stent implantation, the patient was stable, and he then underwent surgery. The coronary stent was extracted, the aortic isthmus was divided, and an extended anastomosis was created. The surgery was performed without complications. On the fourth day, the newborn was transferred from the intensive care unit to the ward, and on the fifteenth day, he was discharged from the hospital in good condition. Hence, palliative stenting is beneficial in newborns with critical aortic coarctation in the decompensated state because it stabilizes and prepares them for subsequent radical surgery, thereby reducing the risk of severe complications and mortality.</p><div><p><strong>Informed consent:</strong> The written informed consent has been obtained from the patient’s parents for this publication.</p><p><strong>Funding:</strong> The study did not have sponsorship.</p><p><strong>Conflict of interest:</strong> Authors declare no conflict of interest.</p><p><strong>Acknowledgment:</strong> We express our gratitude to Melina G. Galstyan for technical support in article writing.</p><p>Received 3 October 2018. Accepted 11 December 2018.</p><p> </p></div>

No abstract