An optimization approach to the problem of protein structure prediction

DOI10.1007/s10107-003-0493-4zbMath1074.92011OpenAlexW2018897936MaRDI QIDQ1764247

Silvia Crivelli, Vincent Lamberti, Teresa Head-Gordon, Elizabeth Eskow, Brett Bader, Robert B. Schnabel, Byrd, Richard H.

Publication date: 24 February 2005

Published in: Mathematical Programming. Series A. Series B (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s10107-003-0493-4

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Related Items

Mathematical programming in computational biology: an annotated bibliography, Some operations research methods for analyzing protein sequences and structures, An optimization approach to the problem of protein structure prediction

Uses Software

• L-BFGS
• CHARMM
• JPred

Cites Work

• On the limited memory BFGS method for large scale optimization
• Application of the renormalization group to deterministic global minimization of molecular conformation energy functions
• The application of the genetic algorithm to the minimization of potential energy functions
• Isotropic effective energy simulated annealing searches for low energy molecular cluster states
• A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing
• An optimization approach to the problem of protein structure prediction
• Parallel continuation-based global optimization for molecular conformation and protein folding
• Nonlinear optimization simplified by hypersurface deformation.
• Distance geometry optimization for protein structures
• Surmounting the multiple-minima problem in protein folding
• Stochastic Methods for Global Optimization
• A modular system of algorithms for unconstrained minimization
• Unnamed Item
• Unnamed Item