Modified genetic algorithm resolves ambiguous NOE restraints and reduces unsightly NOE violations

Proteins: Structure, Function and Genetics

Volumn 39, Issue 4, 2000, Pages 385-392

  Adler, Marc ^a  

^a BAYER AG   (Germany)

Author keywords

Automated NOE assignments; Modified genetic algorithm; NMR structure determination

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; GENETIC ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE;

ALGORITHMS; NEUREGULIN-1; PROTEIN STRUCTURE, TERTIARY;

EID: 0034212903     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000601)39:4<385::AID-PROT110>3.0.CO;2-J     Document Type: Article

References (14)

1. Nilges M. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J Mol Biol 1995;245:645-660.
2. Nilges M, Macias MJ, O'Donoghue SI, Oschkinat H. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol 1997;269:408-422.
3. Fraternali F, Amodeo P, Musco G, Nilges M, Pastore A. Exploring protein interiors: the role of a buried histidine in the KH module fold. Proteins 1999;34:484-496.
4. Mumenthaler C, Braun W. Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. J Mol Biol 1995;254:465-480.
5. Mumenthaler C, Guntert P, Braun W, Wü K. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J Biomol NMR 1997;10:351-362.
6. Xu Y, Wu J, Gorenstein D, Braun W. Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs. J Magn Reson 1999;136:76-85.
7. Beeson NW. An evaluation of the genetic algorithm as a computational NMR tool. Ann Arbor, MI: University Microfilms; 1995.
8. Li KB, Sanctuary BC. Automated resonance assignment of proteins using heteronuclear 3d NMR. Backbone spin systems extraction and creation of polypeptides. J Chem Inform Comp Sci 1997;37:359-366.
9. Brünger A T. X-PLOR Version 3.1: A system for X-ray crystallography and NMR. New Haven: Yale University Press; 1993.
10. Adler M, Thompson SA. The solution structure of heregulin-α and a N-terminal mutant with suppressed activity. Biochem Biophys Res Commun 1999;256:156-161.
11. Jeener J, Meier BH, Bachmann P, Ernst RR. Investigation of the exchange process by two-dimensional NMR spectroscopy. J Chem Phys 1979;71:4546-4553.
12. Kumar A, Ernst RR, Wüthrich K A two-dimensional nuclear enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem Biophys Res Commun 1980;95:1-6.
13. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995;6:277-293.
14. Goldberg DE. Genetic algorithms in search, optimization, and machine learning. Reading, MA: Addison-Wesley; 1989.