PERMOL: Restraint-based protein homology modeling using DYANA or CNS

Bioinformatics

Volumn 21, Issue 9, 2005, Pages 2110-2111

  Möglich, Andreas ^a   Weinfurtner, Daniel ^a   Gronwald, Wolfram ^a   Maurer, Till ^a   Kalbitzer, Hans Robert ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; CALCULATION; COMPUTER PROGRAM; DEVICE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 18744374959     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti276     Document Type: Article

References (11)

1. Brocklehurst,S.M. and Perham,R.N. (1993) Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipoylated H-protein from the pea leaf glycine cleavage system: a new automated method for the prediction of protein tertiary structure. Prot. Sci., 2, 626-639.
2. Brünger,A.T., Adams,P.D., Clore,G.M., DeLano,W.L., Gros,P., Grossekunstleve,R.W., Jiang,J.S., Kuszewski,J., Nilges,M., Pannu,N.S., et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Cryst., D54, 905-921.
3. Gronwald,W. and Kalbitzer,H.R. (2004) Automated structure determination of proteins by NMR spectroscopy. Prog. NMR Spectrosc., 44, 33-96.
4. Güntert,P., Mumenthaler,C. and Wüthrich,K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol., 273, 283-298.
5. Jia,Z., Quail,J.W., Waygood,E.B. and Delbaere,L.T. (1993) The 2.0-A resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination. J. Biol. Chem., 268, 22490-22501.
6. Kolinski,A., Betancourt,M.R., Kihara,D., Rotkiewicz,P. and Skolnick,J. (2001) Generalized comparitive modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins, 44, 133-149.
7. Möglich,A., Koch,B., Hengstenberg,W., Brunner,E., Gronwald,W. and Kalbitzer,H.R. (2004) Solution Structure of the Active-Centre Mutant Ile14Ala of the Histidine-Containing Phosphocarrier Protein (HPr) from Staphylococcus Carnosus. Eur. J. Biochem., 271, 4815-4824.
8. Sali,A. and Blundell,T.L. (1993) Comparitive protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
9. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
10. Uppenberg,J., Svensson,C., Jaki,M., Bertilsson,G., Jendeberg,L. and Berkenstam,A. (1998) Crystal structure of the ligand binding domain of the human nuclear receptor PPARγ. J. Biol. Chem., 273, 31108-31112.
11. Zhang,C., Hou,J. and Kim,S.-H. (2002) Fold prediction of helical proteins using torsion angle dynamics and predicted restraints. Proc, Natl Acad. Sci. USA, 99, 3581-3585.