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Results of the recent Critical Assessment of Techniques for Protein Structure Prediction, CASP8, present several valuable sources of information. First, CASP targets comprise a realistic sample of currently solved protein structures and exemplify the corresponding challenges for predictors. Second, the plethora of predictions by all possible methods(More)
We present an overview of the fifth round of Critical Assessment of Protein Structure Prediction (CASP5) fold recognition category. Prediction models were evaluated by using six different structural measures and four different alignment measures, and these scores were compared to those assigned manually over a diverse subset of target domains. Scores were(More)
BACKGROUND The majority of residues in protein structures are involved in the formation of alpha-helices and beta-strands. These distinctive secondary structure patterns can be used to represent a protein for visual inspection and in vector-based protein structure comparison. Success of such structural comparison methods depends crucially on the accurate(More)
Zinc ®ngers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc ®ngers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell(More)
MOTIVATION Many evolutionarily distant, but functionally meaningful links between proteins come to light through comparison of spatial structures. Most programs that assess structural similarity compare two proteins to each other and find regions in common between them. Structural classification experts look for a particular structural motif instead.(More)
Protein structural domains are necessary for understanding evolution and protein folding, and may vary widely from functional and sequence based domains. Although, various structural domain databases exist, defining domains for some proteins is non-trivial, and definitions of their domain boundaries are not available. Here, we present a novel database of(More)
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