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A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

Title data

Möglich, Andreas ; Weinfurtner, Daniel ; Maurer, Till ; Gronwald, Wolfram ; Kalbitzer, Hans Robert:
A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles.
In: BMC Bioinformatics. Vol. 6 (2005) . - p. 91.
ISSN 1471-2105
DOI: https://doi.org/10.1186/1471-2105-6-91

Abstract in another language

BACKGROUND

We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Doker et al. (1999, BBRC, 257, 348-350). The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS.

RESULTS

To test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor gamma (Ppar gamma). The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar gamma was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms.

CONCLUSION

In summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

Further data

Item Type: Article in a journal
Refereed: Yes
Additional notes: PubMed-ID: 2231712
Institutions of the University: Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry > Chair Biochemistry - Univ.-Prof. Dr. Andreas Möglich
Faculties
Faculties > Faculty of Biology, Chemistry and Earth Sciences
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Professorship Biochemistry
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry
Result of work at the UBT: No
DDC Subjects: 500 Science > 540 Chemistry
Date Deposited: 20 May 2015 07:06
Last Modified: 20 May 2015 07:06
URI: https://eref.uni-bayreuth.de/id/eprint/13613