Jeffrey A. Saunders
Cornell University
9 Papers
268 Citations
Jeffrey A. Saunders is an academic researcher from Cornell University. The author has contributed to research in topics: Protein structure & Protein structure prediction. The author has an hindex of 7, co-authored 9 publications.
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Papers
Recent improvements in prediction of protein structure by global optimization of a potential energy function.
Jaroslaw Pillardy,Cezary Czaplewski,Adam Liwo,Jooyoung Lee,Daniel R. Ripoll,Rajmund Kaźmierkiewicz,Stanisław Ołdziej,William J. Wedemeyer,Kenneth D. Gibson,Yelena A. Arnautova,Jeffrey A. Saunders,Yuan-Jie Ye,Harold A. Scheraga +12 more
TL;DR: The resulting lowest-energy structures of the target proteins agreed with the experimental structures in many respects and constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.
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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.
Stanisław Ołdziej,Cezary Czaplewski,Adam Liwo,M. Chinchio,Marian Nanias,Jorge A. Vila,Mey Khalili,Yelena A. Arnautova,A. Jagielska,Mariusz Makowski,H. D. Schafroth,Rajmund Kaźmierkiewicz,Daniel R. Ripoll,Jaroslaw Pillardy,Jeffrey A. Saunders,Young Kee Kang,Kenneth D. Gibson,Harold A. Scheraga +17 more
TL;DR: For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly alpha-helical protein), the topology of the whole six-helix bundle correctly within 8 A rmsd, except the 32 C-terminal residues, most of which form a beta-hairpin.
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Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets
Jooyoung Lee,Adam Liwo,Adam Liwo,Daniel R. Ripoll,Jaroslaw Pillardy,Jeffrey A. Saunders,Kenneth D. Gibson,Harold A. Scheraga +7 more
TL;DR: In this paper, a hierarchical approach based exclusively on finding the global minimum of an appropriate potential energy function, without the aid of secondary structure prediction, multiple-sequence alignment, or threading, is proposed.
The protein folding problem: global optimization of the force fields.
Harold A. Scheraga,Adam Liwo,S. Oldziej,Cezary Czaplewski,Jaroslaw Pillardy,Daniel R. Ripoll,Jorge A. Vila,R. Kazmierkiewicz,Jeffrey A. Saunders,Yelena A. Arnautova,A. Jagielska,M. Chinchio,Marian Nanias +12 more
TL;DR: The theoretical foundations and the development of a suitable empirical all-atom potential energy function and a global optimization search are examined and a recent attempt to compute a folding pathway is discussed.
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A united residue force-field for calcium–protein interactions
Mey Khalili,Jeffrey A. Saunders,Adam Liwo,Adam Liwo,Stanisław Ołdziej,Stanisław Ołdziej,Harold A. Scheraga +6 more
TL;DR: This force‐field was able to distinguish the EF‐hand motif from all potential binding sites in the crystal structures of bovine α‐lactalbumin, whiting parvalbumin, calbindin D9K, and apo‐calbindinD9K.
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