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. 2007;35(10):3375-82.
doi: 10.1093/nar/gkm251. Epub 2007 May 3.

LOMETS: a local meta-threading-server for protein structure prediction

Sitao Wu  1 , Yang Zhang
Affiliations

LOMETS: a local meta-threading-server for protein structure prediction

Sitao Wu et al. Nucleic Acids Res. 2007.

Abstract

We developed LOMETS, a local threading meta-server, for quick and automated predictions of protein tertiary structures and spatial constraints. Nine state-of-the-art threading programs are installed and run in a local computer cluster, which ensure the quick generation of initial threading alignments compared with traditional remote-server-based meta-servers. Consensus models are generated from the top predictions of the component-threading servers, which are at least 7% more accurate than the best individual servers based on TM-score at a t-test significance level of 0.1%. Moreover, side-chain and C-alpha (C(alpha)) contacts of 42 and 61% accuracy respectively, as well as long- and short-range distant maps, are automatically constructed from the threading alignments. These data can be easily used as constraints to guide the ab initio procedures such as TASSER for further protein tertiary structure modeling. The LOMETS server is freely available to the academic community at http://zhang.bioinformatics.ku.edu/LOMETS.

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Figures

Figure 1.
Figure 1.
TM-score of threading alignments of nine component servers on 620 non-homologous proteins versus the Z-score, where Z-score is defined as the deviation of the inherent raw score from mean divided by the SD. The vertical line in each box indicates a Z-score cutoff to distinguish ‘bad’ and ‘good’ predictions.
Figure 2.
Figure 2.
(a) Average accuracy of predicted Cα and side-chain contacts versus the relative occurrence frequency of the contacts in the LOMETS threading templates. (b) Coverage of the predicted contacts versus the relative occurrence frequency. For each frequency value (f), the data is calculated as an average within the bin of [f − 0.05, f + 0.05].
Figure 3.
Figure 3.
The average result of spatial constraint predictions for ‘Easy’, ‘Medium’ and ‘Hard’ targets on 620 non-homologous proteins. (a) Accuracy of Cα and side-chain center contact predictions. (b) Coverage of Cα and side-chain center contact predictions. (c) Prediction error of short-range and the best long-range distance map.
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