Automatic generation of protein structure cartoons with Pro-origami.

Summary: Protein topology diagrams are 2D representations of protein structure that are particularly useful in understanding and analysing complex protein folds. Generating such diagrams presents a major problem in graph drawing, with automatic approaches often resulting in errors or uninterpretable results. Here we apply a breakthrough in diagram layout to protein topology cartoons, providing clear, accurate, interactive and editable diagrams, which are also an interface to a structural search method.

Adaptive psychophysical procedures, loss functions, and entropy.

In this article, we present a new strategy for locating a point on a psychometric function (threshold determination) for yes-no procedures, called EntFirst. Our results show that it performs better than many existing strategies for estimating the 50% threshold that are commonly used in nonlaboratory settings. We also provide a review of existing algorithms for finding thresholds, with an emphasis on identifying the types of problems for which each algorithm is useful.

Fast and accurate protein substructure searching with simulated annealing and GPUs.

Background: 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.

Results: 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.

Tableau-based protein substructure search using quadratic programming.

Background: Searching for proteins that contain similar substructures is an important task in structural biology. The exact solution of most formulations of this problem, including a recently published method based on tableaux, is too slow for practical use in scanning a large database.

Results: We developed an improved method for detecting substructural similarities in proteins using tableaux.