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

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

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

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 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

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

Additional file 1: Figure S1. of A novel index of protein-protein interface propensity improves interface residue recognition

The Frequency Distribution of ASA for residues on interface and non-interface surface. (PDF 2687 kb

The TM-score of Top1 models selected according to Z-score and M-score for all targets with optimal Z-score <6.0 on SCOP1.75–500 set.

<p>The X-axis and Y-axis of each point represent the TM-score of Top1 models selected according to Z-score and M-score, respectively. Low homology proteins (marked by triangles) had high-quality Top1 models by FR-t5-M (M-score) whereas not FR-t5 (Z-score).</p

Improvement in Low-Homology Template-Based Modeling by Employing a Model Evaluation Method with Focus on Topology

<div><p>Many template-based modeling (TBM) methods have been developed over the recent years that allow for protein structure prediction and for the study of structure-function relationships for proteins. One major problem all TBM algorithms face, however, is their unsatisfactory performance when proteins under consideration are low-homology. To improve the performance of TBM methods for such targets, a novel model evaluation method was developed here, and named MEFTop. Our novel method focuses on evaluating the topology by using two novel groups of features. These novel features included secondary structure element (SSE) contact information and 3-dimensional topology information. By combining MEFTop algorithm with FR-t5, a threading program developed by our group, we found that this modified TBM program, which was named FR-t5-M, exhibited significant improvements in predictive abilities for low-homology protein targets. We further showed that the MEFTop could be a generalized method to improve threading programs for low-homology protein targets. The softwares (FR-t5-M and MEFTop) are available to non-commercial users at our website: <a href="http://jianglab.ibp.ac.cn/lims/FRt5M/FRt5M.html" target="_blank">http://jianglab.ibp.ac.cn/lims/FRt5M/FRt5M.html</a>.</p></div