Protein structure comparison by probability-based matching of secondary structure elements

Protein Structure Comparison Based on Relative Orientation of Secondary Structure Elements

In this paper, a new representation of the protein structure is proposed which facilitates the comparison between protein 3D structures. A representation is proposed based on the orientation of Secondary Structure Elements (SSE’s) of the protein and their axes and inter-direction. The proposed algorithm, Relative Orientation of Secondary Structure (ROSS) is sequence independent and aligns the s...

Automatic Protein Structure Clustering Using Secondary Structure Elements

Modulation of protein-protein interactions by stabilizing/mimicking protein secondary structure elements.

In view of the crucial role of protein-protein intercommunication both in biological and pathological processes, the search of modulators of protein-protein interactions (PPIs) is currently a challenging issue. The development of rational strategies to imitate key secondary structure elements of protein interfaces is complementary to other approaches based on the screening of synthetic or virtu...

BCL::Score—Knowledge Based Energy Potentials for Ranking Protein Models Represented by Idealized Secondary Structure Elements

The topology of most experimentally determined protein domains is defined by the relative arrangement of secondary structure elements, i.e. α-helices and β-strands, which make up 50-70% of the sequence. Pairing of β-strands defines the topology of β-sheets. The packing of side chains between α-helices and β-sheets defines the majority of the protein core. Often, limited experimental datasets re...

GPU-based Visualisation of Protein Secondary Structure

The increasing number of protein 3D structure information available makes the high-quality visualisation of this information play a more and more important role. Beside element-based representations the secondary-structurebased representation – also called cartoon representation – refers to a higher level of abstraction, representing the protein structure as tubes and ribbons. We present a meth...