Journal ArticleDOI
Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete.
Bonnie Berger,Tom Leighton +1 more
TLDR
Theprotein folding problem under the HP model on the cubic lattice is shown to be NP-complete, which means that the protein folding problem belongs to a large set of problems that are believed to be computationally intractable.Abstract:
One of the simplest and most popular biophysical models of protein folding is the hydrophobic-hydrophilic (HP) model. The HP model abstracts the hydrophobic interaction in protein folding by labeling the amino acids as hydrophobic (H for nonpolar) or hydrophilic (P for polar). Chains of amino acids are configured as self-avoiding walks on the 3D cubic lattice, where an optimal conformation maximizes the number of adjacencies between H's. In this paper, the protein folding problem under the HP model on the cubic lattice is shown to be NP-complete. This means that the protein folding problem belongs to a large set of problems that are believed to be computationally intractable.read more
Citations
More filters
Journal ArticleDOI
Ising formulations of many NP problems
TL;DR: This work collects and extends mappings to the Ising model from partitioning, covering and satisfiability, and provides Ising formulations for many NP-complete and NP-hard problems, including all of Karp's 21NP-complete problems.
Journal ArticleDOI
A tutorial for competent memetic algorithms: model, taxonomy, and design issues
Natalio Krasnogor,James C. Smith +1 more
TL;DR: This paper reviews some works on the application of MAs to well-known combinatorial optimization problems, and places them in a framework defined by a general syntactic model, which provides them with a classification scheme based on a computable index D, which facilitates algorithmic comparisons and suggests areas for future research.
Journal ArticleDOI
Finding Low-Energy Conformations of Lattice Protein Models by Quantum Annealing
TL;DR: This report presents a benchmark implementation of quantum annealing for lattice protein folding problems (six different experiments up to 81 superconducting quantum bits) and paves the way towards studying optimization problems in biophysics and statistical mechanics using quantum devices.
Journal ArticleDOI
Simulating Chemistry Using Quantum Computers
TL;DR: This review discusses to what extent the ideas in quantum computation, now a well-established field, have been applied to chemical problems and describes algorithms that achieve significant advantages for the electronic-structure problem, the simulation of chemical dynamics, protein folding, and other tasks.
Journal ArticleDOI
An Immune Algorithm for Protein Structure Prediction on Lattice Models
TL;DR: The proposed immune algorithm inspired by the clonal selection principle for the protein structure prediction problem (PSP) employs two special mutation operators, hypermutation and hypermacromutation to allow effective searching, and an aging mechanism which is a new immune inspired operator that is devised to enforce diversity in the population during evolution.
References
More filters
Journal ArticleDOI
Funnels, pathways, and the energy landscape of protein folding: A synthesis
TL;DR: The work unifies several previously proposed ideas concerning the mechanism protein folding and delimits the regions of validity of these ideas under different thermodynamic conditions.
Journal ArticleDOI
Principles of protein folding--a perspective from simple exact models.
Ken A. Dill,Sarina Bromberg,Kaizhi Yue,Klaus M. Fiebig,David P. Yee,Paul Thomas,Hue Sun Chan +6 more
TL;DR: These studies suggest the possibility of creating “foldable” chain molecules other than proteins, and can account for the properties that characterize protein folding: two‐state cooperativity, secondary and tertiary structures, and multistage folding kinetics.
Journal ArticleDOI
Theory for the folding and stability of globular proteins.
TL;DR: Using lattice statistical mechanics, theory is developed to account for the folding of a heteropolymer molecule such as a protein to the globular and soluble state and the number of accessible conformations is calculated to be an exceedingly small fraction of the number available to the random coil.
Journal ArticleDOI
The protein threading problem with sequence amino acid interaction preferences is NP-complete
TL;DR: This work proves that if both these conditions are allowed then the protein threading decision problem is NP-complete and the related problem of finding the globally optimal proteinthreading isNP-hard, and indicates that computational strategies from other NP- complete problems may be useful for predictive algorithms.
Journal ArticleDOI
Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications.
Ron Unger,John Moult +1 more
TL;DR: A proof that finding the lowest free energy conformation belongs to the class of NP-hard problems is presented and it is suggested that the natural folding process cannot be considered as a search for the global free energy minimum.