TY - JOUR T1 - Fast and accurate methods for predicting short-range constraints in protein models JF - Journal of Computer-Aided Molecular Design Y1 - 2008 A1 - Dominik Gront A1 - Andrzej KoliƄski KW - Algorithms KW - Amino Acid Sequence KW - Models KW - Molecular KW - Molecular Sequence Data KW - Predictive Value of Tests KW - Protein KW - Proteins KW - Proteins: chemistry KW - Proteins: genetics KW - Proteins: metabolism KW - Sequence Analysis KW - Software AB -

Protein modeling tools utilize many kinds of structural information that may be predicted from amino acid sequence of a target protein or obtained from experiments. Such data provide geometrical constraints in a modeling process. The main aim is to generate the best possible consensus structure. The quality of models strictly depends on the imposed conditions. In this work we present an algorithm, which predicts short-range distances between Calpha atoms as well as a set of short structural fragments that possibly share structural similarity with a query sequence. The only input of the method is a query sequence profile. The algorithm searches for short protein fragments with high sequence similarity. As a result a statistics of distances observed in the similar fragments is returned. The method can be used also as a scoring function or a short-range knowledge-based potential based on the computed statistics.

VL - 22 UR - http://www.ncbi.nlm.nih.gov/pubmed/18415023 ER -