TY - JOUR
T1 - Ab initio protein structure prediction of CASP III targets using ROSETTA
AU - Simons, Kim T.
AU - Bonneau, Rich
AU - Ruczinski, Ingo
AU - Baker, David
N1 - Copyright:
Copyright 2004 Elsevier Science B.V., Amsterdam. All rights reserved.
PY - 1999
Y1 - 1999
N2 - To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225). The scoring function used in the simulated annealing procedure consists of sequence-dependent terms representing hydrophobic burial and specific pair interactions such as electrostatics and disulfide bonding and sequence- independent terms representing hard sphere packing, α-helix and β-strand packing, and the collection of β-strands in β-sheets (Simons et al., Proteins 1999;34:82-95). For each of 21 small, ab initio targets, 1,200 final structures were constructed, each the result of 100,000 attempted fragment substitutions. The five structures submitted for the CASP III experiment were chosen from the approximately 25 structures with the lowest scores in the broadest minima (assessed through the number of structural neighbors; Shortle et al., Proc Natl Acad Sci USA 1998;95:1158-1162). The results were encouraging: highlights of the predictions include a 99-residue segment for MarA with an rmsd of 6.4 Å to the native structure, a 95-residue (full length) prediction for the EH2 domain of EPS15 with an rmsd of 6.0 Å, a 75- residue segment of DNAB helicase with an rmsd of 4.7 Å, and a 67-residue segment of ribosomal protein L30 with an rmsd of 3.8 Å. These results suggest that ab initio methods may soon become useful for low-resolution structure prediction for proteins that lack a close homologue of known structure.
AB - To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225). The scoring function used in the simulated annealing procedure consists of sequence-dependent terms representing hydrophobic burial and specific pair interactions such as electrostatics and disulfide bonding and sequence- independent terms representing hard sphere packing, α-helix and β-strand packing, and the collection of β-strands in β-sheets (Simons et al., Proteins 1999;34:82-95). For each of 21 small, ab initio targets, 1,200 final structures were constructed, each the result of 100,000 attempted fragment substitutions. The five structures submitted for the CASP III experiment were chosen from the approximately 25 structures with the lowest scores in the broadest minima (assessed through the number of structural neighbors; Shortle et al., Proc Natl Acad Sci USA 1998;95:1158-1162). The results were encouraging: highlights of the predictions include a 99-residue segment for MarA with an rmsd of 6.4 Å to the native structure, a 95-residue (full length) prediction for the EH2 domain of EPS15 with an rmsd of 6.0 Å, a 75- residue segment of DNAB helicase with an rmsd of 4.7 Å, and a 67-residue segment of ribosomal protein L30 with an rmsd of 3.8 Å. These results suggest that ab initio methods may soon become useful for low-resolution structure prediction for proteins that lack a close homologue of known structure.
KW - Critical assessment of structure prediction experiment (CASP)
KW - Fragment assembly
KW - Knowledge-based scoring functions
KW - Protein structure prediction
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U2 - 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z
DO - 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z
M3 - Article
C2 - 10526365
AN - SCOPUS:0032612579
SN - 0887-3585
VL - 37
SP - 171
EP - 176
JO - Proteins: Structure, Function and Genetics
JF - Proteins: Structure, Function and Genetics
IS - SUPPL. 3
ER -