Comparing bound and unbound protein structures using energy calculation and rotamer statistics

Koch K, Zöllner F, Neumann S, Kummert F, Sagerer G (2002)
In Silico Biology 2(3): 32-32.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Koch, Kerstin; Zöllner, Frank; Neumann, Steffen; Kummert, FranzUniBi; Sagerer, GerhardUniBi
Einrichtung
Research Institute for Cognition and Robotics
Technische Fakultät > AG Angewandte Informatik
Abstract / Bemerkung
Protein data in the PDB covers only a snapshot of a protein structure. For flexible docking conformational changes need to be considered. Rotamer statistics provide the likelihood for side chain conformations, and further comparison of bound and unbound state yields differences in preferred positions. Furthermore, we do a full sampling of selected Chi angles and apply the AMBER force field. Conformation of energy minima comply with the rotamer statistics. Both types of information target the reduction of search space for enumerative docking algorithms and provide parameters for elastic docking.

Key words: Rotamer library, flexible protein-protein docking, energy calculations, AMBER force field, side chain flexibility, flexibility measure

Erscheinungsjahr
2002
Zeitschriftentitel
In Silico Biology
Band
2
Ausgabe
3
Seite(n)
32-32
ISSN
0148-7299
Page URI
https://pub.uni-bielefeld.de/record/1892083

Zitieren

Koch K, Zöllner F, Neumann S, Kummert F, Sagerer G. Comparing bound and unbound protein structures using energy calculation and rotamer statistics. In Silico Biology. 2002;2(3):32-32.
Koch, K., Zöllner, F., Neumann, S., Kummert, F., & Sagerer, G. (2002). Comparing bound and unbound protein structures using energy calculation and rotamer statistics. In Silico Biology, 2(3), 32-32.
Koch, Kerstin, Zöllner, Frank, Neumann, Steffen, Kummert, Franz, and Sagerer, Gerhard. 2002. “Comparing bound and unbound protein structures using energy calculation and rotamer statistics”. In Silico Biology 2 (3): 32-32.
Koch, K., Zöllner, F., Neumann, S., Kummert, F., and Sagerer, G. (2002). Comparing bound and unbound protein structures using energy calculation and rotamer statistics. In Silico Biology 2, 32-32.
Koch, K., et al., 2002. Comparing bound and unbound protein structures using energy calculation and rotamer statistics. In Silico Biology, 2(3), p 32-32.
K. Koch, et al., “Comparing bound and unbound protein structures using energy calculation and rotamer statistics”, In Silico Biology, vol. 2, 2002, pp. 32-32.
Koch, K., Zöllner, F., Neumann, S., Kummert, F., Sagerer, G.: Comparing bound and unbound protein structures using energy calculation and rotamer statistics. In Silico Biology. 2, 32-32 (2002).
Koch, Kerstin, Zöllner, Frank, Neumann, Steffen, Kummert, Franz, and Sagerer, Gerhard. “Comparing bound and unbound protein structures using energy calculation and rotamer statistics”. In Silico Biology 2.3 (2002): 32-32.

3 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.
Kirys T, Ruvinsky AM, Tuzikov AV, Vakser IA., Proteins 80(8), 2012
PMID: 22544766
A major determinant for binding and aminoacylation of tRNA(Ala) in cytoplasmic Alanyl-tRNA synthetase is mutated in dominant axonal Charcot-Marie-Tooth disease.
Latour P, Thauvin-Robinet C, Baudelet-Méry C, Soichot P, Cusin V, Faivre L, Locatelli MC, Mayençon M, Sarcey A, Broussolle E, Camu W, David A, Rousson R., Am J Hum Genet 86(1), 2010
PMID: 20045102
Flexible protein-protein docking based on Best-First search algorithm.
Noy E, Goldblum A., J Comput Chem 31(9), 2010
PMID: 20087902
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