Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

@article{Odziej2005PhysicsbasedPP,
  title={Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.},
  author={Stanisław Ołdziej and Cezary Czaplewski and Adam Liwo and Maurizio Chinchio and Marian Nanias and Jorge A. Vila and Mey Khalili and Yelena A. Arnautova and Anna Jagielska and Mariusz Makowski and Heather D Schafroth and Rajmund Kazmierkiewicz and Daniel R. Ripoll and Jarosław Pillardy and Jeffrey A Saunders and Yun Kenneth Kang and Kenneth D. Gibson and Harold A. Scheraga},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2005},
  volume={102 21},
  pages={7547-52}
}
Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure… CONTINUE READING

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References

Publications referenced by this paper.
Showing 1-10 of 26 references

Proc. Natl. Acad. Sci. USA 102

  • A Liwo, M Khalili, H A Scheraga
  • Proc. Natl. Acad. Sci. USA 102
  • 2005

Polymer

  • C Czaplewski, A Liwo, S Ołdziej, H A Scheraga
  • Polymer
  • 2004

Protein Eng. Des. Selection

  • C Czaplewski, S Ołdziej, A Liwo, H A Scheraga
  • Protein Eng. Des. Selection
  • 2004

Biophys. Chem

  • C Czaplewski, S Rodziewicz-Motowidło, M Da ˛bal, A Liwo, D R Ripoll, H A Scheraga
  • Biophys. Chem
  • 2003

J. Phys. Chem. A

  • S Ołdziej, U Kozłowska, A Liwo, H A Scheraga
  • J. Phys. Chem. A
  • 2003

J. Phys. Chem. B

  • K Maksimiak, S Rodziewicz-Motowidło, C Czaplewski, A Liwo, H A Scheraga
  • J. Phys. Chem. B
  • 2003

Proc. Natl. Acad. Sci. USA 100

  • M Nanias, M Chinchio, J Pillardy, D R Ripoll, H A Scheraga
  • Proc. Natl. Acad. Sci. USA 100
  • 2003

Proteins Struct. Func. Genet

  • J Moult, K Fidelis, A Zemla, T Hubbard
  • Proteins Struct. Func. Genet
  • 2003

Proteins Struct. Funct. Genet

  • P Aloy, A Stark, A Hadley, R B Rusell
  • Proteins Struct. Funct. Genet
  • 2003

J. Comp. Chem

  • H A Scheraga, J Pillardy, +5 authors Y A Arnautova
  • J. Comp. Chem
  • 2002

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