Literature DB >> 8281132

Complexity of protein folding.

A S Fraenkel1.   

Abstract

It is believed that the native folded three-dimensional conformation of a protein is its lowest free energy state, or one of its lowest. It is shown here that both a two- and three-dimensional mathematical model describing the folding process as a free energy minimization problem is NP-hard. This means that the problem belongs to a large set of computational problems, assumed to be very hard ("conditionally intractable"). Some of the possible ramifications of this result are speculated upon.

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Year:  1993        PMID: 8281132     DOI: 10.1007/BF02460704

Source DB:  PubMed          Journal:  Bull Math Biol        ISSN: 0092-8240            Impact factor:   1.758


  9 in total

1.  Quantum cryptography without Bell's theorem.

Authors: 
Journal:  Phys Rev Lett       Date:  1992-02-03       Impact factor: 9.161

Review 2.  Biochemical topology: applications to DNA recombination and replication.

Authors:  S A Wasserman; N R Cozzarelli
Journal:  Science       Date:  1986-05-23       Impact factor: 47.728

Review 3.  Accurate simulation of protein dynamics in solution.

Authors:  M Levitt; R Sharon
Journal:  Proc Natl Acad Sci U S A       Date:  1988-10       Impact factor: 11.205

4.  Principles that govern the folding of protein chains.

Authors:  C B Anfinsen
Journal:  Science       Date:  1973-07-20       Impact factor: 47.728

5.  Refinement of protein conformations using a macromolecular energy minimization procedure.

Authors:  M Levitt; S Lifson
Journal:  J Mol Biol       Date:  1969-12-14       Impact factor: 5.469

6.  Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications.

Authors:  R Unger; J Moult
Journal:  Bull Math Biol       Date:  1993-11       Impact factor: 1.758

Review 7.  Structural domains in proteins and their role in the dynamics of protein function.

Authors:  J Janin; S J Wodak
Journal:  Prog Biophys Mol Biol       Date:  1983       Impact factor: 3.667

Review 8.  Stability of proteins. Proteins which do not present a single cooperative system.

Authors:  P L Privalov
Journal:  Adv Protein Chem       Date:  1982

Review 9.  Stability of proteins: small globular proteins.

Authors:  P L Privalov
Journal:  Adv Protein Chem       Date:  1979
  9 in total
  10 in total

1.  Graphically-enabled integration of bioinformatics tools allowing parallel execution.

Authors:  K H Cheung; P Miller; A Sherman; S Weston; E Stratmann; M Schultz; M Snyder; A Kumar
Journal:  Proc AMIA Symp       Date:  2000

2.  Differential evolution for protein folding optimization based on a three-dimensional AB off-lattice model.

Authors:  Borko Bošković; Janez Brest
Journal:  J Mol Model       Date:  2016-09-30       Impact factor: 1.810

3.  Parallel computation with molecular-motor-propelled agents in nanofabricated networks.

Authors:  Dan V Nicolau; Mercy Lard; Till Korten; Falco C M J M van Delft; Malin Persson; Elina Bengtsson; Alf Månsson; Stefan Diez; Heiner Linke; Dan V Nicolau
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-22       Impact factor: 11.205

Review 4.  The Last Secret of Protein Folding: The Real Relationship Between Long-Range Interactions and Local Structures.

Authors:  Aoneng Cao
Journal:  Protein J       Date:  2020-10-10       Impact factor: 2.371

5.  Finding the lowest free energy conformation of a protein is an NP-hard problem: proof and implications.

Authors:  R Unger; J Moult
Journal:  Bull Math Biol       Date:  1993-11       Impact factor: 1.758

6.  Landscape encodings enhance optimization.

Authors:  Konstantin Klemm; Anita Mehta; Peter F Stadler
Journal:  PLoS One       Date:  2012-04-09       Impact factor: 3.240

Review 7.  Something has to give: scaling combinatorial computing by biological agents exploring physical networks encoding NP-complete problems.

Authors:  Falco C M J M van Delft; Giulia Ipolitti; Dan V Nicolau; Ayyappasamy Sudalaiyadum Perumal; Ondřej Kašpar; Sara Kheireddine; Sebastian Wachsmann-Hogiu; Dan V Nicolau
Journal:  Interface Focus       Date:  2018-10-19       Impact factor: 3.906

8.  Using synchronized oscillators to compute the maximum independent set.

Authors:  Antik Mallick; Mohammad Khairul Bashar; Daniel S Truesdell; Benton H Calhoun; Siddharth Joshi; Nikhil Shukla
Journal:  Nat Commun       Date:  2020-09-17       Impact factor: 14.919

Review 9.  Why do proteins aggregate? "Intrinsically insoluble proteins" and "dark mediators" revealed by studies on "insoluble proteins" solubilized in pure water.

Authors:  Jianxing Song
Journal:  F1000Res       Date:  2013-03-22

10.  A continuous-time MaxSAT solver with high analog performance.

Authors:  Botond Molnár; Ferenc Molnár; Melinda Varga; Zoltán Toroczkai; Mária Ercsey-Ravasz
Journal:  Nat Commun       Date:  2018-11-19       Impact factor: 14.919

  10 in total

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