New error measures and methods for realizing protein graphs from distance data

DOI10.1007/s00454-016-9846-7zbMath1358.05085arXiv1607.00868WikidataQ62562115 ScholiaQ62562115MaRDI QIDQ517453

Claudia D'Ambrosio, Leo Liberti, Carlile C. Lavor, K. H. Vu, Nelson F. Maculan

Publication date: 23 March 2017

Published in: Discrete \& Computational Geometry (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1607.00868

zbMATH Keywords

distance geometry; mathematical programming; protein conformation

Mathematics Subject Classification ID

05C90: Applications of graph theory

90C22: Semidefinite programming

90C20: Quadratic programming

05C10: Planar graphs; geometric and topological aspects of graph theory

92D20: Protein sequences, DNA sequences

05C12: Distance in graphs

Uses Software

• Matlab
• AMPL
• YALMIP
• COIN-OR
• Mosek
• Ipopt
• SNLSDP
• PhaseLift