Recent improvements in prediction of protein structure by global optimization of a potential energy function
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- Jarosław Pillardy
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Cezary Czaplewski
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Adam Liwo
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Jooyoung Lee
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Daniel R. Ripoll
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Rajmund Kaźmierkiewicz
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Stanisław Ołdziej
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- William J. Wedemeyer
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Kenneth D. Gibson
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Yelena A. Arnautova
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Jeff Saunders
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Yuan-Jie Ye
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
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- Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland; and Cornell Theory Center, Ithaca, NY 14853-3801
Description
<jats:p> Recent improvements of a hierarchical <jats:italic>ab initio</jats:italic> or <jats:italic>de novo</jats:italic> approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (C <jats:sup>α</jats:sup> ) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å C <jats:sup>α</jats:sup> rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the C <jats:sup>α</jats:sup> rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a C <jats:sup>α</jats:sup> rmsd less than 6.0 Å. Overall, these results constitute an important step toward the <jats:italic>ab initio</jats:italic> prediction of protein structure <jats:italic>solely</jats:italic> from the amino acid sequence. </jats:p>
Journal
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- Proceedings of the National Academy of Sciences
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Proceedings of the National Academy of Sciences 98 (5), 2329-2333, 2001-02-20
Proceedings of the National Academy of Sciences
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Details 詳細情報について
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- CRID
- 1360574094356796928
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- ISSN
- 10916490
- 00278424
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- Data Source
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- Crossref