Literature DB >> 12163065

Energy estimation in protein design.

Joaquim Mendes1, Raphael Guerois, Luis Serrano.   

Abstract

The progress achieved by several groups in the field of computational protein design shows that successful design methods include two major features: efficient algorithms to deal with the combinatorial exploration of sequence space and optimal energy functions to rank sequences according to their fitness for the given fold.

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Year:  2002        PMID: 12163065     DOI: 10.1016/s0959-440x(02)00345-7

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  20 in total

1.  Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation.

Authors:  Navin Pokala; Tracy M Handel
Journal:  Protein Sci       Date:  2004-03-09       Impact factor: 6.725

2.  Molecular dynamics simulation of amyloid beta dimer formation.

Authors:  B Urbanc; L Cruz; F Ding; D Sammond; S Khare; S V Buldyrev; H E Stanley; N V Dokholyan
Journal:  Biophys J       Date:  2004-10       Impact factor: 4.033

3.  Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles.

Authors:  Benjamin D Allen; Alex Nisthal; Stephen L Mayo
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-02       Impact factor: 11.205

4.  One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations.

Authors:  Shannon A Marshall; Christina L Vizcarra; Stephen L Mayo
Journal:  Protein Sci       Date:  2005-03-31       Impact factor: 6.725

5.  Computational thermostabilization of an enzyme.

Authors:  Aaron Korkegian; Margaret E Black; David Baker; Barry L Stoddard
Journal:  Science       Date:  2005-05-06       Impact factor: 47.728

6.  Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions.

Authors:  Hoang T Tran; Rohit V Pappu
Journal:  Biophys J       Date:  2006-06-09       Impact factor: 4.033

7.  A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining.

Authors:  Taner Z Sen; Haitao Cheng; Andrzej Kloczkowski; Robert L Jernigan
Journal:  Protein Sci       Date:  2006-09-25       Impact factor: 6.725

8.  Combinatorial methods for small-molecule placement in computational enzyme design.

Authors:  Jonathan Kyle Lassila; Heidi K Privett; Benjamin D Allen; Stephen L Mayo
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-30       Impact factor: 11.205

9.  Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model.

Authors:  Liang-Tsung Huang; M Michael Gromiha; Shinn-Ying Ho
Journal:  J Mol Model       Date:  2007-03-30       Impact factor: 1.810

Review 10.  Challenges in the computational design of proteins.

Authors:  María Suárez; Alfonso Jaramillo
Journal:  J R Soc Interface       Date:  2009-03-11       Impact factor: 4.118

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