Fast and accurate protein substructure searching with simulated annealing and GPUs

<p>Abstract</p> <p>Background</p> <p>Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioinformatics. While there are many existing methods for structural similarity searching, faster and more accurate approaches are still required, and few current methods are capable of substructure (motif) searching.</p> <p>Results</p> <p>We developed an improved heuristic for tableau-based protein structure and substructure searching using simulated annealing, that is as fast or faster and comparable in accuracy, with some widely used existing methods. Furthermore, we created a parallel implementation on a modern graphics processing unit (GPU).</p> <p>Conclusions</p> <p>The GPU implementation achieves up to 34 times speedup over the CPU implementation of tableau-based structure search with simulated annealing, making it one of the fastest available methods. To the best of our knowledge, this is the first application of a GPU to the protein structural search problem.</p

Factors associated with topographic changes of the optic nerve head induced by acute intraocular pressure reduction in glaucoma patients

Purpose To investigate factors associated with changes in optic nerve head (ONH) topography after acute intraocular pressure (IOP) reduction in patients with primary open-angle glaucoma (POAG).Methods Untreated POAG patients (IOP >21 mm Hg) were prospectively enrolled. Systemic and ocular information were collected, including central corneal thickness (CCT) and corneal hysteresis (CH). All patients underwent confocal scanning laser ophthalmoscopy and tonometry (Goldmann) before and 1 h after pharmacological IOP reduction. the mean of three measurements was considered for analysis. Changes in each ONH topographic parameter were assessed (one eye was randomly selected), and those that changed significantly were correlated with patient's systemic and ocular characteristics.Results A total of 42 patients were included (mean age, 66.7 +/- 11.8 years). After a mean IOP reduction of 47.3 +/- 11.9%, significant changes were observed in cup area and volume, and in rim area and volume (P = 0.21, P = 0.12). Including all significant factors in a multivariable model, only the presence of diabetes remained significantly associated with all ONH parameters evaluated (P < 0.01).Conclusions Different systemic and ocular factors, such as diabetes, CH, and the relative size of the cup, seem to be associated with the magnitude of changes in ONH topography after acute IOP reduction in POAG patients. These associations partially explain the ONH changes observed in these patients and suggest that other factors are possibly implicated in an individual susceptibility to IOP. Eye (2011) 25, 201-207; doi:10.1038/eye.2010.179; published online 3 December 2010Universidade Federal de São Paulo, Dept Ophthalmol, BR-820 São Paulo, BrazilNew York Eye & Ear Infirm, Einhorn Clin Res Ctr, New York, NY 10003 USANew York Med Coll, Valhalla, NY 10595 USAUniversidade Federal de São Paulo, Dept Ophthalmol, BR-820 São Paulo, BrazilWeb of Scienc