Protein Folding in the Hydrophobic-Hydrophilic (<i>HP</i>) Model is NP-Complete

Berger, Bonnie; Leighton, Tom

doi:10.1089/cmb.1998.5.27

Cited by 350 publications

(201 citation statements)

References 11 publications

Supporting

Mentioning

195

Contrasting

Unclassified

Order By: Relevance

“…is typically an example of NP-complete problems, a class of NP-hard problems (see, e.g., Berger and Leighton 1998) that are at the core of combinatorial optimization theory (Mezard et al 2002). The asymmetric mechanism described here offers a way to explore efficiently a drastically (but intelligently) reduced search space, if the initial set of elements to be assigned can be subdivided into two chemically distinct subsets (classes).…”

Section: Conclusion and Perspectivementioning

confidence: 99%

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Delarue¹

2006

RNA

View full text Add to dashboard Cite

Aminoacyl-tRNA synthetases (aaRSs) are responsible for creating the pool of correctly charged aminoacyl-tRNAs that are necessary for the translation of genetic information (mRNA) by the ribosome. Each aaRS belongs to either one of only two classes with two different mechanisms of aminoacylation, making use of either the 29OH (Class I) or the 39OH (Class II) of the terminal A76 of the tRNA and approaching the tRNA either from the minor groove (29OH) or the major groove (39OH). Here, an asymmetric pattern typical of differentiation is uncovered in the partition of the codon repertoire, as defined by the mechanism of aminoacylation of each corresponding tRNA. This pattern can be reproduced in a unique cascade of successive binary decisions that progressively reduces codon ambiguity. The deduced order of differentiation is manifestly driven by the reduction of translation errors. A simple rule can be defined, decoding each codon sequence in its binary class, thereby providing both the code and the key to decode it. Assuming that the partition into two mechanisms of tRNA aminoacylation is a relic that dates back to the invention of the genetic code in the RNA World, a model for the assignment of amino acids in the codon table can be derived. The model implies that the stop codon was always there, as the codon whose tRNA cannot be charged with any amino acid, and makes the prediction of an ultimate differentiation step, which is found to correspond to the codon assignment of the 22nd amino acid pyrrolysine in archaebacteria.

show abstract

Section: Conclusion and Perspectivementioning

confidence: 99%

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Delarue¹

2006

RNA

View full text Add to dashboard Cite

show abstract

“…As simple as this model seems to be, it has been proven to be an NP-complete problem in two and three dimensions [8]. Therefore, sophisticated algorithms were applied to find lowest energy states for chains of up to 136 monomers.…”

Section: Introductionmentioning

confidence: 99%

Exact sequence analysis for three-dimensional hydrophobic-polar lattice proteins

Schiemann

Bachmann

Janke

2005

The Journal of Chemical Physics

View full text Add to dashboard Cite

We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a non-degenerate ground state. Furthermore we were interested in characteristic thermodynamic properties of HP proteins with designing sequences. In order to be able to perform these exact studies, we applied an efficient enumeration method based on contact sets.

show abstract

“…Although the HP model is extremely simple, it has been proven that identifying native conformations is an NP-complete problem in two and three dimensions [10]. Therefore, sophisticated algorithms were developed to find lowest-energy states for chains of up to 136 monomers.…”

Section: The Hydrophobic-polar (Hp) Lattice Protein Modelmentioning

confidence: 99%

Thermodynamics of Protein Folding from Coarse-Grained Models’ Perspectives

Bachmann

Janke

Rugged Free Energy Landscapes

View full text Add to dashboard Cite

Protein Folding in the Hydrophobic-Hydrophilic (HP) Model is NP-Complete

Cited by 350 publications

References 11 publications

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Exact sequence analysis for three-dimensional hydrophobic-polar lattice proteins

Thermodynamics of Protein Folding from Coarse-Grained Models’ Perspectives

Contact Info

Product

Resources

About