Geodesic
The Use of Refmac Crystallographic Refinement Program for Detection of Alternative Conformations in Biological Macromolecules
Matematičeskaâ biologiâ i bioinformatika, Tome 7 (2012) no. 2, pp. 692-702 
Oleg V. Sobolev; Vladimir Yu. Lunin. The Use of Refmac Crystallographic Refinement Program for Detection of Alternative Conformations in Biological Macromolecules. Matematičeskaâ biologiâ i bioinformatika, Tome 7 (2012) no. 2, pp. 692-702. http://geodesic.mathdoc.fr/item/MBB_2012_7_2_a17/
@article{MBB_2012_7_2_a17,
     author = {Oleg V. Sobolev and Vladimir Yu. Lunin},
     title = {The {Use} of {Refmac} {Crystallographic} {Refinement} {Program} for {Detection} of {Alternative} {Conformations} in {Biological} {Macromolecules}},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
     pages = {692--702},
     year = {2012},
     volume = {7},
     number = {2},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MBB_2012_7_2_a17/}
}
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Voir la notice de l'article provenant de la source Math-Net.Ru

The analysis of the shifts of atomic centers in unrestrained crystallographic refinement of macromolecular structure enables the detection of alternative conformations of polypeptide chain fragments. Decision-making procedures of the presence or absence of alternative conformations for a particular fragment are based on statistical analysis of atomic shifts obtained during the trial unrestrained refinement of large number of protein structures. The analysis also showed that probability distributions of atomic shifts appear to depend on the program used for refinement, so the decision making procedures should be adapted to the refinement program. The construction of databases with atomic shifts, their analysis and the development of automatic decision-making procedures for detection of alternative conformations with the use of popular refinement program Refmac are described in this paper.

[1] Howard E. I., Sanishvili R., Cachau R. E., Mitschler A., Chevrier B., Barth P., Lamour V., Van Zandt M., Sibley E., Bon C., Moras D., Schneider T. R., Joachimiak A., Podjarny A., Proteins, 55 (2004), 792–804 | DOI

[2] Ševčík J., Dauter Z., Wilson K. S., Acta Crystallographica D, 60 (2004), 1198–1204

[3] Wang J., Dauter M., Alkire R., Joachimiak A., Dauter Z., Acta Crystallographica D, 63 (2007), 1254–1268

[4] Rypniewski W. R., Østergaard P., Nørregaard-Madsen M., Dauter M., Wilson K. S., Acta Crystallographica D, 57 (2001), 8–19

[5] Getzoff E. D., Gutwin K. N., Genick U. K., Nat. Struct. Biol., 10 (2003), 663–668 | DOI

[6] Kursula I., Wierenga R. K., J. Biol. Chem., 278 (2003), 9544–9551 | DOI

[7] Addlagatta A., Krzywda S., Czapinska H., Otlewski J., Jaskolski M., Acta Crystallographica D, 57 (2001), 649–663

[8] Dauter Z., Sierer L. C., Wilson K. S., Acta Crystallographica D, 48 (1992), 42–59

[9] Dodd F. E., Hasnain S. S., Acta Crystallographica D, 51 (1995), 1052–1064

[10] Koepke J., Scharff E. I., Lücke C., Rüterjans H., Fritzsch G., Acta Crystallographica D, 59 (2003), 1744–1754

[11] Sobolev O. V., Lunin V. Yu., Matematicheskaya biologiya i bioinformatika, 3 (2008), 50–59 (data obrascheniya: 21.12.2012) http://www.matbio.org/downloads/Sobolev2008(3_50).pdf

[12] Sobolev O. V., Lunin V. Y., Acta Crystallographica D, 68 (2012), 1118–1127

[13] Sobolev O. V., Computational Crystallography Newsletter, 3 (2012), 32–34

[14] Afonine P. V., Grosse-Kunstleve R. W., Echols N., Headd J. J., Moriarty N. W., Mustyakimov M., Terwilliger T. C., Urzhumtsev A., Zwart P. H., Adams P. D., Acta Crystallographica D, 68 (2012), 352–367

[15] Murshudov G. N., Skubak P., Lebedev A. A., Pannu N. S., Steiner R. A., Nicholls R. A., Winn M. D., Long F., Vagin A. A., Acta Crystallographica D, 67 (2011), 355–367

[16] Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E., Nucleic Acids Res., 28 (2000), 235–242 | DOI | MR

[17] Noivirt-Brik O., Prilusky J., Sussman J. L., Proteins, 77:9, Suppl. (2009), 210–216 | DOI

[18] Fawcett T., Pattern Recognition Letters, 27 (2006), 861–874 | DOI

[19] Antson A. A., Smith D. J., Roper D. I., Lewis S., Caves L. S., Verma C. S., Buckley S. L., Lillford P. J., Hubbard R. E., J. Mol. Biol., 305 (2010), 875–889 | DOI