Literature DB >> 20700821

Automated detection of problem restraints in NMR data sets using the FINGAR genetic algorithm method.

D A Pearlman1.   

Abstract

The recently described FINGAR genetic algorithm method for NMR refinement [D.A. Pearlman (1996) J. Biomol. NMR, 8, 67-76] has been extended so that it can be used to detect problem restraints in an NMR-derived set of data. A problem restraint is defined as a restraint in a generally well-behaved set where the associated target value is in error, due to inaccuracies in the data, misassignment, etc. The method described here, FINGAR.RWF, locates problem restraints by finding those restraints that, if removed from the data set, result in a disproportionate improvement in the scoring function. The method is applied to several test cases of simulated data, as well as to real data for the FK506 macrocycle, with excellent results.

Entities:  

Year:  1999        PMID: 20700821     DOI: 10.1023/A:1008351824432

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  16 in total

Review 1.  Protein structure determination in solution by NMR spectroscopy.

Authors:  K Wüthrich
Journal:  J Biol Chem       Date:  1990-12-25       Impact factor: 5.157

2.  Deviation versus violation plots: A new technique for assessing the self-consistency of NMR data.

Authors:  M Adler
Journal:  J Biomol NMR       Date:  1996-12       Impact factor: 2.835

3.  FINGAR: A new genetic algorithm-based method for fitting NMR data.

Authors:  D A Pearlman
Journal:  J Biomol NMR       Date:  1996-07       Impact factor: 2.835

Review 4.  Two-, three-, and four-dimensional NMR methods for obtaining larger and more precise three-dimensional structures of proteins in solution.

Authors:  G M Clore; A M Gronenborn
Journal:  Annu Rev Biophys Biophys Chem       Date:  1991

5.  Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.

Authors:  A E Torda; R M Scheek; W F van Gunsteren
Journal:  J Mol Biol       Date:  1990-07-05       Impact factor: 5.469

6.  How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches.

Authors:  D A Pearlman
Journal:  J Biomol NMR       Date:  1994-01       Impact factor: 2.835

Review 7.  Two-dimensional NMR and protein structure.

Authors:  A Bax
Journal:  Annu Rev Biochem       Date:  1989       Impact factor: 23.643

8.  Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry.

Authors:  C Mumenthaler; W Braun
Journal:  J Mol Biol       Date:  1995-12-01       Impact factor: 5.469

9.  Predicting the helix packing of globular proteins by self-correcting distance geometry.

Authors:  C Mumenthaler; W Braun
Journal:  Protein Sci       Date:  1995-05       Impact factor: 6.725

10.  An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.

Authors:  D Zhao; O Jardetzky
Journal:  J Mol Biol       Date:  1994-06-24       Impact factor: 5.469

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