Improved protein surface comparison and application to low-resolution protein structure data

Protein structure comparison using bipartite graph matching and its application to protein structure classification.

A measure of protein structure similarity is calculated from the matching of pairs of secondary structure elements between two proteins. The interaction of each pair was estimated from their axial line segments and combined with other geometric features to produce an optimal discrimination between intrafamily and interfamily relationships. The matching used a fast bipartite graph-matching algor...

alpha-Surface and Its Application to Mining Protein Data

Given a finite set of points in three dimensional Euclidean space , the subset that forms its surface could be different when observed in different levels of details. In this paper, we introduce a notion called -surface. We present an algorithm that extracts the -surface from a finite set of points in . We apply the algorithm to extracting the surfaces of proteins and discover patterns from the...

-Surface and Its Application to Mining Protein Data

Given a finite set of points in three dimensional Euclidean space , the subset that forms its surface could be different when observed in different levels of details. In this paper, we introduce a notion called -surface. We present an algorithm that extracts the -surface from a finite set of points in . We apply the algorithm to extracting the surfaces of proteins and discover patterns from the...

Application of statistical potentials to protein structure refinement from low resolution ab initio models.

Recently ab initio protein structure prediction methods have advanced sufficiently so that they often assemble the correct low resolution structure of the protein. To enhance the speed of conformational search, many ab initio prediction programs adopt a reduced protein representation. However, for drug design purposes, better quality structures are probably needed. To achieve this refinement, i...

Linking Low Resolution Protein Folds to Biochemical Relevance: Accurate Protein Structure, Dynamics and Thermodynamics