M. Chinchio
Cornell University
9 Papers
360 Citations
M. Chinchio is an academic researcher from Cornell University. The author has contributed to research in topics: Protein structure prediction & Global optimization. The author has an hindex of 6, co-authored 9 publications. Previous affiliations of M. Chinchio include University of Gdańsk.
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Papers
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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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
Stanisław Ołdziej,Justyna Ła̧giewka,Adam Liwo,Cezary Czaplewski,M. Chinchio,and Marian Nanias,Harold A. Scheraga +6 more
TL;DR: The application of the hierarchical optimization method of protein potential-energy landscapes described in the accompanying papers to optimize the UNRES potential energy function was successful and the target function composed of con...
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field.
TL;DR: A potential function developed to model disulfide bonds is coupled with the united-residue (UNRES) force field, and used in both canonical and replica exchange molecular dynamics simulations to produce complete oxidative folding pathways.
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Packing helices in proteins by global optimization of a potential energy function
TL;DR: The results for 42 proteins show that the approach reproduces native-like folds of α-helical proteins as low-energy local minima of this highly simplified potential function.
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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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