Predicting novel protein folds by using FRAGFOLD

The results of applying a fragment‐based protein tertiary structure prediction method to the prediction of 8 CASP4 targets are described. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm. Despite the significant degree of success in this case, there is clearly much more developmental work required before predictions with the accuracy of a good homology model, or even a good fold recognition model, can be made with use of this kind of approach. Proteins 2001;Suppl 5:127–132. © 2002 Wiley‐Liss, Inc.

[1]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[2]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[3]  D. T. Jones,et al.  A new approach to protein fold recognition , 1992, Nature.

[4]  V. Mutt,et al.  NK‐lysin, a novel effector peptide of cytotoxic T and NK cells. Structure and cDNA cloning of the porcine form, induction by interleukin 2, antibacterial and antitumour activity. , 1995, The EMBO journal.

[5]  L. Kelley,et al.  An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. , 1996, Protein engineering.

[6]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[7]  David T. Jones.  Successful ab initio prediction of the tertiary structure of NK‐lysin using multiple sequences and recognized supersecondary structural motifs , 1997, Proteins.

[8]  D. T. Jones,et al.  Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure , 1999, Proteins.

[9]  Richard Bonneau,et al.  Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.

[10]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[11]  David C. Jones,et al.  GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.

[12]  M. Maqueda,et al.  Bacteriocin AS-48, a microbial cyclic polypeptide structurally and functionally related to mammalian NK-lysin. , 2000, Proceedings of the National Academy of Sciences of the United States of America.