| Dokumentenart: | Artikel | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Titel eines Journals oder einer Zeitschrift: | BMC bioinformatics | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Verlag: | BMC | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ort der Veröffentlichung: | LONDON | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Band: | 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Seitenbereich: | S. 91 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Datum: | 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Zusätzliche Informationen (Öffentlich): | online-Ressource | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Institutionen: | Biologie und Vorklinische Medizin > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Dr. Hans Robert Kalbitzer | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Stichwörter / Keywords: | CONTAINING PHOSPHOCARRIER PROTEIN; PROLIFERATOR-ACTIVATED RECEPTORS; NMR STRUCTURE CALCULATION; LIGAND-BINDING DOMAIN; STRUCTURE PREDICTION; STAPHYLOCOCCUS-CARNOSUS; STRUCTURAL GENOMICS; 3-DIMENSIONAL STRUCTURE; RESOLUTION STRUCTURE; SEQUENCE ALIGNMENT; | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dewey-Dezimal-Klassifikation: | 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Status: | Veröffentlicht | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Begutachtet: | Unbekannt / Keine Angabe | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| An der Universität Regensburg entstanden: | Unbekannt / Keine Angabe | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dokumenten-ID: | 16625 |
Web of ScienceZusammenfassung
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 ...
Zusammenfassung
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.
Metadaten zuletzt geändert: 29 Sep 2021 07:38
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