Geodesic
Analyzing the data bank of proteins' space structures (PDB): a geometrical approach
Fundamentalʹnaâ i prikladnaâ matematika, Tome 20 (2015) no. 3, pp. 33-46 
E. A. Vilkul; A. O. Ivanov; A. S. Mishchenko; Th. Yu. Popelenskii; A. A. Tuzhilin; K. V. Shaytan. Analyzing the data bank of proteins' space structures (PDB): a geometrical approach. Fundamentalʹnaâ i prikladnaâ matematika, Tome 20 (2015) no. 3, pp. 33-46. http://geodesic.mathdoc.fr/item/FPM_2015_20_3_a1/
@article{FPM_2015_20_3_a1,
     author = {E. A. Vilkul and A. O. Ivanov and A. S. Mishchenko and Th. Yu. Popelenskii and A. A. Tuzhilin and K. V. Shaytan},
     title = {Analyzing the data bank of proteins' space structures {(PDB):} a~geometrical approach},
     journal = {Fundamentalʹna\^a i prikladna\^a matematika},
     pages = {33--46},
     year = {2015},
     volume = {20},
     number = {3},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/FPM_2015_20_3_a1/}
}
TY  - JOUR
AU  - E. A. Vilkul
AU  - A. O. Ivanov
AU  - A. S. Mishchenko
AU  - Th. Yu. Popelenskii
AU  - A. A. Tuzhilin
AU  - K. V. Shaytan
TI  - Analyzing the data bank of proteins' space structures (PDB): a geometrical approach
JO  - Fundamentalʹnaâ i prikladnaâ matematika
PY  - 2015
SP  - 33
EP  - 46
VL  - 20
IS  - 3
UR  - http://geodesic.mathdoc.fr/item/FPM_2015_20_3_a1/
LA  - ru
ID  - FPM_2015_20_3_a1
ER  - 
%0 Journal Article
%A E. A. Vilkul
%A A. O. Ivanov
%A A. S. Mishchenko
%A Th. Yu. Popelenskii
%A A. A. Tuzhilin
%A K. V. Shaytan
%T Analyzing the data bank of proteins' space structures (PDB): a geometrical approach
%J Fundamentalʹnaâ i prikladnaâ matematika
%D 2015
%P 33-46
%V 20
%N 3
%U http://geodesic.mathdoc.fr/item/FPM_2015_20_3_a1/
%G ru
%F FPM_2015_20_3_a1

Voir la notice de l'article provenant de la source Math-Net.Ru

A geometrical approach to the analysis of a data bank containing information on space structures of proteins is suggested. As a result of the analysis, several relationships concerning possible conformations are found, and also there is obtained a list of polypeptides whose structures differ essentially from typical concepts of the 3D-structure of proteins. Those deviations could indicate possible errors and gaps of the interpreting models in use, as well as some new unknown relations and rules.

[1] Vilkul E. A., Tuzhilin A. A., “Geometriya aminokislot i polipeptidov: sluchai rentgenostrukturnogo analiza”, Nanostruktury. Matem. fiz. i modelirovanie, 11:2 (2014), 5–27

[2] Ivanov A. O., Mischenko A. S., Tuzhilin A. A., “Geometriya aminokislot i polipeptidov”, Nanostruktury. Matem. fiz. i modelirovanie, 10:1 (2014), 39–47

[3] Ivanov A. O., Mischenko A. S., Tuzhilin A. A., “Geometriya lomanykh i polipeptidov”, Nanostruktury. Matem. fiz. i modelirovanie, 10:1 (2014), 49–76

[4] Shaitan K. V., “Relaksatsionnaya model idealnogo foldinga v odnorodno vyazkoi srede”, Biofizika, 60:5 (2015), 843–852

[5] Shaitan K. V., Orshanskii I. V., “Molekulyarnaya dinamika samoorganizatsii i reologicheskaya model superspiralnoi struktury protofibrilly volokna pautiny”, Biofizika, 60:4 (2015), 656–660

[6] Shults G., Shirmer R., Printsipy strukturnoi organizatsii belkov, Mir, M., 1982

[7] Amunts A., Brown A., Toots J., Scheres S. H. W., Ramakrishnan V., “The structure of the human mitochondrial ribosome”, Science, 348 (2015), 95–98 | DOI

[8] Branden C. I., Jones T., “Between objectivity and subjectivity”, Nature, 343 (1990), 687–689 | DOI

[9] Hammond C., The Basics of Crystallography and Diffraction, Oxford Univ. Press, Oxford, 2009

[10] Hooft R. W. W., Vriend G., Sander C., Abola E. E., “Errors in protein structures”, Nature, 381 (1996), 272–272 | DOI

[11] Ivanov A. O., Mishchenko A. S., Tuzhilin A. A., “Critical analysis of amino acids and polypeptides geometry”, Continuous and Distributed Systems: Theory and Applications, v. 2, eds. V. A. Sadovnichiy, M. Z. Zgurovsky, Springer, Berlin, 2015, 29–74 | MR

[12] Protein Data Bank. An Information Portal, http://www.rcsb.org/pdb/home/home.do

[13] Protein Data Bank. An Information Portal. 2PDE., http://www.rcsb.org/pdb/explore.do?structureId=2pde

[14] Wüthrich K., “Protein recognition by NMR”, Nature Struct. Biol., 7 (2000), 188–189 | DOI