We have developed an automatic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallographers as a standard-of-truth. Comparison to the currently ...

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...

A method for finding protein folds consistent with secondary structure assignments and imposed experimental restraints is described. All possible matches between the query pattern and every member of a database of protein structural domains are generated by a comparison of secondary structure assignments. The comparison allows for errors in predicted secondary structure elements and possible va...

We have developed a hybrid system to predict the secondary structures (alpha-helix, beta-sheet and coil) of proteins and achieved 66.4% accuracy, with correlation coefficients of C(coil) = 0.429, C alpha = 0.470 and C beta = 0.387. This system contains three subsystems ("experts"): a neural network module, a statistical module and a memory-based reasoning module. First, the three experts indepe...