The alignment accuracies for FR-t5 and FR-t3 on SALIGN and MUSTER190 datasets.

a<p>Mean value and the standard error (estimated by bootstrap simulation on 10,000 re-sampling of the dataset).</p

Coarse-grained Structure Model of a 9-residue Fragment.

<p>The coarse-grained structure of a 9-residue fragment consists of nine points, each of which represents an amino acid and is denoted as the Cα atom of the residue. A link between two Cα atoms is a virtual bond that connects the two residues. Thus, the description of the coarse-grained structure of a 9-residue fragment follows that for 3-residue fragment (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017215#pone-0017215-g002" target="_blank">Figure 2</a>). The bold letters , denote the bisecting vector of and , the bisecting vector of and , respectively. , denote the vectors in a plane defined by three continuous atoms (,, and ), and (,, and ), respectively.</p

MOESM1 of Analysis and expression of the carotenoid biosynthesis genes from Deinococcus wulumuqiensis R12 in engineered Escherichia coli

Additional file 1: Figure S1. Gene function annotations of R12 genome in GO, COG and KEGG databases. Figure S2. The antiSMASH analysis results of R12 genome. Figure S3. The orientation and distribution of the carotenoid biosynthetic genes from the R1 and R12. Table S1. Bioinformatic analysis of key enzymes of carotenoid biosynthesis in R12. Table S2. Percentages of sequence identity of proteins in carotenoid biosynthesis between D. wulumuqiensis R12 and other Deinococcus spp

The benchmarking of the sensitivity of FR-t5 and FR-t3 on Lindahl dataset.

<p>The benchmarking of the sensitivity of FR-t5 and FR-t3 on Lindahl dataset.</p

A Schematic Diagram of Spatial Representation and Conformational Constraints of a 3-residue Fragment.

<p>The bold letters and denote the bisecting vector of and , the bisecting vector of and , respectively. and denote the vectors in planes defined by three backbone atoms (,, and ), and (,, and ), respectively.</p

The comparison of FR-t5 with other methods for fold recognition on the Lindahl benchmark.

a<p>this work.</p>b, c<p>Results are cited from from Refs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017215#pone.0017215-Cheng1" target="_blank">[32]</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017215#pone.0017215-Zhang1" target="_blank">[11]</a>, respectively.</p><p>*The best results are marked by asterisk.</p

The alignment accuracy (%) of FR-t5 on the SALIGN test data.

<p>Since the programs BLAST, COMPASS, SALIGN, SPARKS, SP3, UNI-FOLD have all been tested on the SALIGN test data previously, for comparison, their results were taken from the previous studies: BLAST, COMPASS, and SALIGN from Marti-Renom et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017215#pone.0017215-MartiRenom1" target="_blank">[29]</a>, SPARKS and SP3 from Zhou and Zhou <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017215#pone.0017215-Zhou2" target="_blank">[9]</a>, and UNI-FOLD from Poleksic and Fienup <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017215#pone.0017215-Poleksic1" target="_blank">[39]</a>.</p

Modeled structures for three CASP9 targets, T0549, T0592 and T0553, by FR-t5.

<p>(a) The superposition between the native structure of T0549 (green) and the top1 model (red) predicted by FR-t5. (b) The superposition between the native structure of T0592 (green) and the top1 model (red) predicted by FR-t5. (c) The superposition between the native structure of T0553 (green) and the top1 model (red) generated by FR-t5.</p