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Threading As a Tool For Ab Initio Prediction Of 3D Folds Of Proteins: Possibility And Limitations Dmitry S. Rykunov Institute of Theoretical & Experimental Biophysics RAS, Pushchino, Moscow reg., 142292 Russia Aim: Our aim is to apply threading approach to ab initioprediction of protein folds. As the target folds for treading, we use the sets of folding patterns that are partly observed and partly not observed in natural protein. Each set is obtained from some native protein core using extrapolations of its secondary structure elements and all the reasonable modifications of the core topology, i.e. a variety chain pathways through this core. The computations are based on the self consistent molecular field theory and on the statistical mechanics of chain molecules. The molecular field summarizes the action of long-range interactions. Statistical mechanics finds the stable state and fluctuations of the chain in this field. Results: The developed computer program and the set of generated frameworks are used to single out the stable folds of a number of protein chains. It is shown that extrapolation of secondary structure segments improves recognition of cognate proteins, and that extension of target fold library by reconnectingof secondary structures of known protein folds is useful for recognition of "new", previously not observed protein folds. However, in a general case the native fold is recognized as one of the most stable, but rarely as the most stable chain fold. ## Back to the list of abstracts