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TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model.

Veeramalai M, Ye Y, Godzik A - BMC Bioinformatics (2008)

Bottom Line: Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses.For beta-rich proteins its accuracy is better than FATCAT, because the TOPS+ strings models contains important information of the parallel and anti-parallel hydrogen-bond patterns between the beta-strand SSEs (Secondary Structural Elements).We show that the TOPS++FATCAT errors, rare as they are, can be clearly linked to oversimplifications of the TOPS diagrams and can be corrected by the development of more precise secondary structure element definitions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Joint Center for Molecular Modeling, Burnham Institute for Medical Research, La Jolla, CA 92037, USA. mallikav@burnham.org

ABSTRACT

Background: Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have managed to capture the intuitive understanding of protein structures developed in structural biology, especially in the context of rapid database searches. Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses.

Results: We developed a TOPS++FATCAT algorithm that uses an intuitive description of the proteins' structures as captured in the popular TOPS diagrams to limit the search space of the aligned fragment pairs (AFPs) in the flexible alignment of protein structures performed by the FATCAT algorithm. The TOPS++FATCAT algorithm is faster than FATCAT by more than an order of magnitude with a minimal cost in classification and alignment accuracy. For beta-rich proteins its accuracy is better than FATCAT, because the TOPS+ strings models contains important information of the parallel and anti-parallel hydrogen-bond patterns between the beta-strand SSEs (Secondary Structural Elements). We show that the TOPS++FATCAT errors, rare as they are, can be clearly linked to oversimplifications of the TOPS diagrams and can be corrected by the development of more precise secondary structure element definitions.

Software availability: The benchmark analysis results and the compressed archive of the TOPS++FATCAT program for Linux platform can be downloaded from the following web site: http://fatcat.burnham.org/TOPS/ CONCLUSION: TOPS++FATCAT provides FATCAT accuracy and insights into protein structural changes at a speed comparable to sequence alignments, opening up a possibility of interactive protein structure similarity searches.

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Related in: MedlinePlus

The ROC curve analysis results based on P-values obtained from flexible and rigid options from the FATCAT and TOPS++FATCAT methods, where rF-pvalue and fF-pvalue indicate rigid and flexible FATCAT methods, respectively; similarly, rT2F-pavlue and fT2F-pvalue represents rigid and flexible TOPS++FATCAT methods, respectively.
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Figure 5: The ROC curve analysis results based on P-values obtained from flexible and rigid options from the FATCAT and TOPS++FATCAT methods, where rF-pvalue and fF-pvalue indicate rigid and flexible FATCAT methods, respectively; similarly, rT2F-pavlue and fT2F-pvalue represents rigid and flexible TOPS++FATCAT methods, respectively.

Mentions: We have compared the performance of the TOPS++FATCAT method against the original FATCAT method using the SCOP classification information at the superfamily level. We have plotted the ROC curves based on P-values obtained from the FATCAT and the TOPS++FATCAT methods. We have plotted the ROC curves separately for the main SCOP classes, i.e., all-alpha, all-beta, alpha/beta, alpha+beta, and all proteins regardless of the class they belong to (see Figure 5(a) to 5(e)). In the graph, the x- and y-axes represent the false positive and true positive rates of the performance of the comparison methods respectively. In the legend, rF-pvalue and fF-pvalue indicate results from the rigid and flexible FATCAT methods, respectively; similarly, rT2F-pvalue and fT2F-pvalue represent the rigid and flexible TOPS++FATCAT methods, respectively. We have calculated the AUC values for all the SCOP classes based on ROC curves obtained from the FATCAT and TOPS++FATCAT methods with the flexible/rigid options (see Table 2).


TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model.

Veeramalai M, Ye Y, Godzik A - BMC Bioinformatics (2008)

The ROC curve analysis results based on P-values obtained from flexible and rigid options from the FATCAT and TOPS++FATCAT methods, where rF-pvalue and fF-pvalue indicate rigid and flexible FATCAT methods, respectively; similarly, rT2F-pavlue and fT2F-pvalue represents rigid and flexible TOPS++FATCAT methods, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553092&req=5

Figure 5: The ROC curve analysis results based on P-values obtained from flexible and rigid options from the FATCAT and TOPS++FATCAT methods, where rF-pvalue and fF-pvalue indicate rigid and flexible FATCAT methods, respectively; similarly, rT2F-pavlue and fT2F-pvalue represents rigid and flexible TOPS++FATCAT methods, respectively.
Mentions: We have compared the performance of the TOPS++FATCAT method against the original FATCAT method using the SCOP classification information at the superfamily level. We have plotted the ROC curves based on P-values obtained from the FATCAT and the TOPS++FATCAT methods. We have plotted the ROC curves separately for the main SCOP classes, i.e., all-alpha, all-beta, alpha/beta, alpha+beta, and all proteins regardless of the class they belong to (see Figure 5(a) to 5(e)). In the graph, the x- and y-axes represent the false positive and true positive rates of the performance of the comparison methods respectively. In the legend, rF-pvalue and fF-pvalue indicate results from the rigid and flexible FATCAT methods, respectively; similarly, rT2F-pvalue and fT2F-pvalue represent the rigid and flexible TOPS++FATCAT methods, respectively. We have calculated the AUC values for all the SCOP classes based on ROC curves obtained from the FATCAT and TOPS++FATCAT methods with the flexible/rigid options (see Table 2).

Bottom Line: Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses.For beta-rich proteins its accuracy is better than FATCAT, because the TOPS+ strings models contains important information of the parallel and anti-parallel hydrogen-bond patterns between the beta-strand SSEs (Secondary Structural Elements).We show that the TOPS++FATCAT errors, rare as they are, can be clearly linked to oversimplifications of the TOPS diagrams and can be corrected by the development of more precise secondary structure element definitions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Joint Center for Molecular Modeling, Burnham Institute for Medical Research, La Jolla, CA 92037, USA. mallikav@burnham.org

ABSTRACT

Background: Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have managed to capture the intuitive understanding of protein structures developed in structural biology, especially in the context of rapid database searches. Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses.

Results: We developed a TOPS++FATCAT algorithm that uses an intuitive description of the proteins' structures as captured in the popular TOPS diagrams to limit the search space of the aligned fragment pairs (AFPs) in the flexible alignment of protein structures performed by the FATCAT algorithm. The TOPS++FATCAT algorithm is faster than FATCAT by more than an order of magnitude with a minimal cost in classification and alignment accuracy. For beta-rich proteins its accuracy is better than FATCAT, because the TOPS+ strings models contains important information of the parallel and anti-parallel hydrogen-bond patterns between the beta-strand SSEs (Secondary Structural Elements). We show that the TOPS++FATCAT errors, rare as they are, can be clearly linked to oversimplifications of the TOPS diagrams and can be corrected by the development of more precise secondary structure element definitions.

Software availability: The benchmark analysis results and the compressed archive of the TOPS++FATCAT program for Linux platform can be downloaded from the following web site: http://fatcat.burnham.org/TOPS/ CONCLUSION: TOPS++FATCAT provides FATCAT accuracy and insights into protein structural changes at a speed comparable to sequence alignments, opening up a possibility of interactive protein structure similarity searches.

Show MeSH
Related in: MedlinePlus