Building Fragment Library Based on Fold Recognition for Protein Structure Prediction
Fragment assembly method is an important approach for ab initio prediction of the three-dimensional structure of proteins.The current method for building fragment library,which is strongly based on sequence similarity,lowers the prediction accuracy for those remote homologous targets.It is an important task to find the fragments with high structural similarity to the native protein structures for building high-quality fragment libraries.We take advantage of structural similarity defined in SCOP database and predict the SCOP fold for the predicting target.The structure information extracted from the proteins whose structures are released and SCOP fold is the same with the predicting target can be combined into a database of residue fragments(Vall database).A new fragment library is produced based on a comprehensive evaluation between the residue fragments of the target protein and Vall database.Such new fragment library is employed by the parallel ant colonies for backbone prediction.Evaluation is conducted by comparing our fragment library to the old fragment library used by typical methods of protein structure prediction.The experimental results indicate that our approach can find more near native conformations for the target.