Accurate modeling of protein conformation by automatic segment matching.

Abstract

Segment match modeling uses a data base of highly refined known protein X-ray structures to build an unknown target structure from its amino acid sequence and the atomic coordinates of a few of its atoms (generally only the C alpha atoms). The target structure is first broken into a set of short segments. The data base is then searched for matching segments, which are fitted onto the framework of the target structure. Three criteria are used for choosing a matching data base segment: amino acid sequence similarity, conformational similarity (atomic co-ordinates), and compatibility with the target structure (van der Waals' interactions). The new method works surprisingly well: for eight test proteins ranging in size from 46 to 323 residues, the all-atom root-mean-square deviation of the modeled structures is between 0.93 A and 1.73 A (the average is 1.26 A). Deviations of this magnitude are comparable with those found for protein co-ordinates before and after refinement against X-ray data or for co-ordinates of the same protein in different crystal packings. These results are insensitive to errors in the C alpha positions or to missing C alpha atoms: accurate models can be built with C alpha errors of up to 1 A or by using only half the C alpha atoms. The fit to the X-ray structures is improved significantly by building several independent models based on different random choices and then averaging co-ordinates; this novel concept has general implications for other modeling tasks. The segment match modeling method is fully automatic, yields a complete set of atomic co-ordinates without any human intervention and is efficient (14 s/residue on the Silicon Graphics 4D/25 Personal Iris workstation.

Extracted Key Phrases

18 Figures and Tables

050100'95'97'99'01'03'05'07'09'11'13'15'17
Citations per Year

1,260 Citations

Semantic Scholar estimates that this publication has 1,260 citations based on the available data.

See our FAQ for additional information.

Cite this paper

@article{Levitt1992AccurateMO, title={Accurate modeling of protein conformation by automatic segment matching.}, author={Michael Levitt}, journal={Journal of molecular biology}, year={1992}, volume={226 2}, pages={507-33} }