29 research outputs found
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure
No full textBackground: Although multiple templates are frequently used in comparative modeling, the effect of inclusion of additional template(s) on model accuracy (when compared to that of corresponding single-template based models) is not clear. To address this, we systematically analyze two-template models, the simplest case of multiple-template modeling. For an existing target-template pair (single-template modeling), a two-template based model of the target sequence is constructed by including an additional template without changing the original alignment to measure the effect of the second template on model accuracy. Results: Even though in a large number of cases a two-template model showed higher accuracy than the corresponding one-template model, over the entire dataset only a marginal improvement was observed on average, as there were many cases where no change or the reverse change was observed. The increase in accuracy due to the structural complementarity of the templates increases at higher alignment accuracies. The combination of templates showing the highest potential for improvement is that where both templates share similar and low (less than 30%) sequence identity with the target, as well as low sequence identity with each other. The structural similarity between the templates also helps in identifying template combinations having a higher chance of resulting in an improved model. Conclusion: Inclusion of additional template(s) does not necessarily improve model quality, but there are distinct combinations of the two templates, which can be selected a priori, that tend to show improvement in model quality over the single template model. The benefit derived from the structural complementarity is dependent on the accuracy of the modeling alignment. The study helps to explain the observation that a careful selection of templates together with an accurate target:template alignment are necessary to the benefit from using multiple templates in comparative modeling and provides guidelines to maximize the benefit from using multiple templates. This enables formulation of simple template selection rules to rank targets of a protein family in the context of structural genomics
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure-4
No full text�� -1 Å; or neutral: 1 Å > Δ RMSD > -1 Å. In all plots only models based on template combinations for which S1–S2 is less than 5% are included. The ratio between the number of Good and Bad STR models as a function of S3, the sequence identity between the templates. The good/bad ratio as a function of the RMSD between the two templates. The good/bad ratio as a function of the RMSD between the two templates; in these plots the additional restriction of S3 < 30% is imposed on all selected models with the aim of showing the complementarity between S3 and template RMSD selection.<p><b>Copyright information:</b></p><p>Taken from "Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure"</p><p>http://www.biomedcentral.com/1472-6807/8/31</p><p>BMC Structural Biology 2008;8():31-31.</p><p>Published online 16 Jul 2008</p><p>PMCID:PMC2483983.</p><p></p
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure-3
No full textSing structure-based alignments (RMSD- RMSD) as a function of Target:Template1 sequence identity (S1) for different ranges of [S1–S2]. The colored circles green, yellow, blue to red are in increasing order of [S1–S2]. The absence of data at lower sequence identity (for yellow, blue and red) is due to the fact that for large values [S1 – S2], small S1 is not possible. Difference in RMSD for models built using structure-based alignments (RMSD- RMSD) as a function of Target:Template1 sequence identity (S1) for different ranges of S3. The colored circles, green, blue to red, are in the increasing order of S3. Only models with S1 similar to S2 are shown here. The absence of data points (green and blue) for higher sequence identity is due to the fact that certain combinations of S1, S2, and S3 are not possible.<p><b>Copyright information:</b></p><p>Taken from "Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure"</p><p>http://www.biomedcentral.com/1472-6807/8/31</p><p>BMC Structural Biology 2008;8():31-31.</p><p>Published online 16 Jul 2008</p><p>PMCID:PMC2483983.</p><p></p
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure-2
No full textCles) is shown as a function of SEQ alignment accuracy. The STR curve represents the maximum achievable structural complementarity for each alignment accuracy bin. Difference between the observed structural complementarity in SEQ models (ΔRMSD) and maximum achievable structural complementarity (ΔRMSD) as a function of SEQ alignment accuracy.<p><b>Copyright information:</b></p><p>Taken from "Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure"</p><p>http://www.biomedcentral.com/1472-6807/8/31</p><p>BMC Structural Biology 2008;8():31-31.</p><p>Published online 16 Jul 2008</p><p>PMCID:PMC2483983.</p><p></p
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure-1
No full textSEQ.2.1 (small gray circle). Comparison between single and two-template STR models, STR.2.2 (filled circle) and STR.2.1 (small gray circle). The lower sequence identity region is highlighted in the inset. Because of the large number of cases analyzed (> 10,000 models per curve) even the small differences shown here are statistically significant based on the Student t test. Thus, for clarity no error bars are shown. Distribution of difference in RMSD between one-template (STR.2.1) and two-template models (STR.2.2) built using structure-based alignments (RMSD- RMSD). Only models with S1 ≤ 40% are shown here.<p><b>Copyright information:</b></p><p>Taken from "Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure"</p><p>http://www.biomedcentral.com/1472-6807/8/31</p><p>BMC Structural Biology 2008;8():31-31.</p><p>Published online 16 Jul 2008</p><p>PMCID:PMC2483983.</p><p></p
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure-5
No full textS2 less than 5%, S1 < 30%, S3 < 30% and template RMSD between 3.5 and 5.5 Å are shown here. The dark bars correspond to Good models (see figure 6 legend), the empty bars to Bad models, the light bars to Neutral models. Fraction of Neutral (unchanged), Good and Bad models in the dataset before and after applying the template selection criteria described above.<p><b>Copyright information:</b></p><p>Taken from "Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure"</p><p>http://www.biomedcentral.com/1472-6807/8/31</p><p>BMC Structural Biology 2008;8():31-31.</p><p>Published online 16 Jul 2008</p><p>PMCID:PMC2483983.</p><p></p
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure-0
No full textEs (top). The Target segment corresponding to the box has no structural information in absence of Template2. ALN stands for alignment type (SEQuence or STRucture). The total improvement of multiple template models over single template models is a combination of decreasing alignment errors and structural complementarity.<p><b>Copyright information:</b></p><p>Taken from "Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure"</p><p>http://www.biomedcentral.com/1472-6807/8/31</p><p>BMC Structural Biology 2008;8():31-31.</p><p>Published online 16 Jul 2008</p><p>PMCID:PMC2483983.</p><p></p
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure-7
No full textEs (top). The Target segment corresponding to the box has no structural information in absence of Template2. ALN stands for alignment type (SEQuence or STRucture). The total improvement of multiple template models over single template models is a combination of decreasing alignment errors and structural complementarity.<p><b>Copyright information:</b></p><p>Taken from "Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure"</p><p>http://www.biomedcentral.com/1472-6807/8/31</p><p>BMC Structural Biology 2008;8():31-31.</p><p>Published online 16 Jul 2008</p><p>PMCID:PMC2483983.</p><p></p
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure-6
No full textof selected SEQ models (empty circles) is shown as a function of SEQ alignment accuracy. The curve for all SEQ models from Figure 4A (black circles) is shown for comparison. Difference between observed structural complementarity in SEQ models (ΔRMSD) and maximum achievable structural complementarity (ΔRMSD) as a function of SEQ alignment accuracy is shown for the selected models (empty circles) and for all models (black circles).<p><b>Copyright information:</b></p><p>Taken from "Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure"</p><p>http://www.biomedcentral.com/1472-6807/8/31</p><p>BMC Structural Biology 2008;8():31-31.</p><p>Published online 16 Jul 2008</p><p>PMCID:PMC2483983.</p><p></p
Retracted: C4d deposition in native kidney disease and its correlation with proteinuria and serum urea/creatinine
No full textThe article titled, "C4d deposition in native kidney disease and its correlation with proteinuria and serum urea/creatinine", published in the International Journal of Research in Medical Sciences, Volume 6, Issue 12, 2018, Pages 3935-3941, DOI: http://dx.doi.org/10.18203/2320-6012.ijrms20184886 is being retracted. We received complaint from one of the co-authors, after publication of the article that corresponding author, Dr. Sant Pandey had submitted the manuscript without informing other co-authors and it was not his original work. We contacted the corresponding author who could not satisfactorily respond to our queries. Since the author could not satisfactorily defend his paper and contravened the declaration he made while submitting his manuscript, it was decided to retract the article from International Journal of Research in Medical Sciences and not to consider any manuscript submitted by him in future
