Combining local‐structure, fold‐recognition, and new fold methods for protein structure prediction

This article presents an overview of the SAM‐T02 method for protein fold recognition and the UNDERTAKER program for ab initio predictions. The SAM‐T02 server is an automatic method that uses two‐track hidden Markov models (HMMS) to find and align template proteins from PDB to the target protein. The two‐track HMMs use an amino acid alphabet and one of several different local structure alphabets. The UNDERTAKER program is a new fragment‐packing program that can use short or long fragments and alignments to create protein conformations. The HMMs and fold‐recognition alignments from the SAM‐T02 method were used to generate the fragment and alignment libraries used by UNDERTAKER. We present results on a few selected targets for which this combined method worked particularly well: T0129, T0181, T0135, T0130, and T0139. Proteins 2003;53:491–496. © 2003 Wiley‐Liss, Inc.

[1]  J F Gibrat,et al.  Surprising similarities in structure comparison. , 1996, Current opinion in structural biology.

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

[3]  C Sander,et al.  Predicting protein structure using hidden Markov models , 1997, Proteins.

[4]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[5]  Anders Krogh,et al.  SAM: SEQUENCE ALIGNMENT AND MODELING SOFTWARE SYSTEM , 1995 .

[6]  Marc A. Martí-Renom,et al.  EVA: continuous automatic evaluation of protein structure prediction servers , 2001, Bioinform..

[7]  M. Pugnière,et al.  Peptide and ester synthesis in organic solvents catalyzed by seryl proteases linked to alumina , 1986, Proteins.

[8]  Richard Bonneau,et al.  Rosetta in CASP4: Progress in ab initio protein structure prediction , 2001, Proteins.

[9]  Yutaka Kuroda,et al.  Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation. , 2002, Journal of molecular biology.

[10]  K. Karplus,et al.  Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry , 2003, Proteins.

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

[12]  Richard Hughey,et al.  Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..

[13]  K Karplus,et al.  Predicting protein structure using only sequence information , 1999, Proteins.

[14]  K Karplus,et al.  What is the value added by human intervention in protein structure prediction? , 2001, Proteins.

[15]  C Kooperberg,et al.  Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.

[16]  H. M. Einspahr,et al.  Crystallization of purified recombinant human interleukin‐1β , 1988, Proteins.

[17]  P. Argos,et al.  Knowledge‐based protein secondary structure assignment , 1995, Proteins.