Literature DB >> 10542084

Folding alphabets.

H S Chan1.   

Abstract

A new computational approach optimizes searches for reduced protein folding alphabets that use fewer than 20 types of amino acids. The predicted optimal five-letter alphabet happens to be in agreement with the suggestive results of a recent experiment, but whether highly reduced alphabets are sufficient for truly protein-like properties remains an open experimental question.

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Year:  1999        PMID: 10542084     DOI: 10.1038/14876

Source DB:  PubMed          Journal:  Nat Struct Biol        ISSN: 1072-8368


  20 in total

1.  Evolvability and single-genotype fluctuation in phenotypic properties: a simple heteropolymer model.

Authors:  Tao Chen; David Vernazobres; Tetsuya Yomo; Erich Bornberg-Bauer; Hue Sun Chan
Journal:  Biophys J       Date:  2010-06-02       Impact factor: 4.033

2.  Comparing folding codes in simple heteropolymer models of protein evolutionary landscape: robustness of the superfunnel paradigm.

Authors:  Richard Wroe; Erich Bornberg-Bauer; Hue Sun Chan
Journal:  Biophys J       Date:  2004-10-22       Impact factor: 4.033

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

Authors:  Marc Delarue
Journal:  RNA       Date:  2006-12-12       Impact factor: 4.942

4.  A method for computing the inter-residue interaction potentials for reduced amino acid alphabet.

Authors:  Abhinav Luthra; Anupam Nath Jha; G K Ananthasuresh; Saraswathi Vishveswara
Journal:  J Biosci       Date:  2007-08       Impact factor: 1.826

5.  Amino acid partitioning using a Fiedler vector model.

Authors:  S J Shepherd; C B Beggs; S Jones
Journal:  Eur Biophys J       Date:  2007-07-04       Impact factor: 1.733

6.  Funneling and frustration in the energy landscapes of some designed and simplified proteins.

Authors:  Ha H Truong; Bobby L Kim; Nicholas P Schafer; Peter G Wolynes
Journal:  J Chem Phys       Date:  2013-09-28       Impact factor: 3.488

7.  Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space.

Authors:  David B Dahl; Zach Bohannan; Qianxing Mo; Marina Vannucci; Jerry Tsai
Journal:  J Mol Biol       Date:  2008-02-29       Impact factor: 5.469

8.  A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.

Authors:  C Etchebest; C Benros; A Bornot; A-C Camproux; A G de Brevern
Journal:  Eur Biophys J       Date:  2007-06-13       Impact factor: 1.733

9.  Biophysics of protein evolution and evolutionary protein biophysics.

Authors:  Tobias Sikosek; Hue Sun Chan
Journal:  J R Soc Interface       Date:  2014-11-06       Impact factor: 4.118

10.  HMM_RA: an improved method for alpha-helical transmembrane protein topology prediction.

Authors:  Jing Hu; Changhui Yan
Journal:  Bioinform Biol Insights       Date:  2008-01-31
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