%0 Journal Article %J Proteins %D 1997 %T Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns %A Wei-Ping Hu %A Andrzej Koliński %A Jeffrey Skolnick %K Amino Acid %K Amino Acid Sequence %K Amino Acids %K Amino Acids: chemistry %K Data Interpretation %K Models %K Molecular %K Molecular Sequence Data %K Protein Structure %K Proteins %K Proteins: chemistry %K Reproducibility of Results %K Secondary %K Sequence Alignment %K Sequence Alignment: methods %K Sequence Alignment: statistics & numerical data %K Sequence Homology %K Statistical %X A new and more accurate method has been developed for predicting the backbone U-turn positions (where the chain reverses global direction) and the dominant secondary structure elements between U-turns in globular proteins. The current approach uses sequence-specific secondary structure propensities and multiple sequence information. The latter plays an important role in the enhanced success of this approach. Application to two sets (total 108) of small to medium-sized, single-domain proteins indicates that approximately 94% of the U-turn locations are correctly predicted within three residues, as are 88% of dominant secondary structure elements. These results are significantly better than our previous method (Kolinski et al., Proteins 27:290-308, 1997). The current study strongly suggests that the U-turn locations are primarily determined by local interactions. Furthermore, both global length constraints and local interactions contribute significantly to the determination of the secondary structure types between U-turns. Accurate U-turn predictions are crucial for accurate secondary structure predictions in the current method. Protein structure modeling, tertiary structure predictions, and possibly, fold recognition should benefit from the predicted structural data provided by this new method. %B Proteins %V 29 %P 443–460 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/9408942 %0 Journal Article %J Proteins %D 1997 %T A method for the prediction of surface "U"-turns and transglobular connections in small proteins %A Andrzej Koliński %A Jeffrey Skolnick %A Adam Godzik %A Wei-Ping Hu %K Algorithms %K Amino Acid Sequence %K Animals %K Humans %K Molecular Sequence Data %K Protein Folding %K Protein Structure %K Proteins %K Proteins: chemistry %K Secondary %X A simple method for predicting the location of surface loops/turns that change the overall direction of the chain that is, "U" turns, and assigning the dominant secondary structure of the intervening transglobular blocks in small, single-domain globular proteins has been developed. Since the emphasis of the method is on the prediction of the major topological elements that comprise the global structure of the protein rather than on a detailed local secondary structure description, this approach is complementary to standard secondary structure prediction schemes. Consequently, it may be useful in the early stages of tertiary structure prediction when establishment of the structural class and possible folding topologies is of interest. Application to a set of small proteins of known structure indicates a high level of accuracy. The prediction of the approximate location of the surface turns/loops that are responsible for the change in overall chain direction is correct in more than 95% of the cases. The accuracy for the dominant secondary structure assignment for the linear blocks between such surface turns/loops is in the range of 82%. %B Proteins %V 27 %P 290–308 %8 feb %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/9061792