Automated backbone assignment of labeled proteins using the threshold accepting algorithm

Michael Leutner, Ruth M. Gschwind, Jens Liermann, Christian Schwarz, Gerd Gemmecker, Horst Kessler

Publikation: Beitrag in FachzeitschriftArtikelBegutachtung

88 Zitate (Scopus)

Abstract

The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein Assignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment of proteins, based on the analysis of NMR backbone resonances plus Cβ information. In order to overcome the problems caused by peak overlap and missing signals in an automated assignment process, PASTA uses threshold accepting, a combinatorial optimization strategy, which is superior to simulated annealing due to generally faster convergence and better solutions. The reliability of this algorithm is shown by reproducing the complete sequential backbone assignment of several proteins from published NMR data. The robustness of the algorithm against misassigned signals, noise, spectral overlap and missing peaks is shown by repeating the assignment with reduced sequential information and increased chemical shift tolerances. The performance of the program on real data is finally demonstrated with automatically picked peak lists of human nonpancreatic synovial phospholipase A2, a protein with 124 residues.

OriginalspracheEnglisch
Seiten (von - bis)31-43
Seitenumfang13
FachzeitschriftJournal of Biomolecular NMR
Jahrgang11
Ausgabenummer1
DOIs
PublikationsstatusVeröffentlicht - 1998

Fingerprint

Untersuchen Sie die Forschungsthemen von „Automated backbone assignment of labeled proteins using the threshold accepting algorithm“. Zusammen bilden sie einen einzigartigen Fingerprint.

Dieses zitieren