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Inverse Protein Folding Problem via Quadratic Programming

Andrii Riazanov 1, 2 Mikhail Karasikov 1, 2 Sergei Grudinin 3 
3 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, Grenoble INP - Institut polytechnique de Grenoble - Grenoble Institute of Technology, LJK - Laboratoire Jean Kuntzmann
Abstract : This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the polypeptide chain using the tertiary structure of a molecule. Unknown amino acids are determined according to the principle of energy minimization. This study represents inverse folding problem as a quadratic optimization problem and uses different relaxation techniques to reduce it to the problem of convex optimizations. Computational experiment compares the quality of these approaches on real protein structures.
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Submitted on : Tuesday, January 3, 2017 - 11:10:10 AM
Last modification on : Friday, April 29, 2022 - 8:14:03 AM
Long-term archiving on: : Tuesday, April 4, 2017 - 1:05:41 PM


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  • HAL Id : hal-01419374, version 2
  • ARXIV : 1701.00673



Andrii Riazanov, Mikhail Karasikov, Sergei Grudinin. Inverse Protein Folding Problem via Quadratic Programming. Information Technology and Systems 2016, Sep 2016, Repino, St. Petersburg, Russia. pp.561-568. ⟨hal-01419374v2⟩



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