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CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events.

Kumar S, Ratnikov BI, Kazanov MD, Smith JW, Cieplak P - PLoS ONE (2015)

Bottom Line: The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results.All this information will provide the user with perspectives in reasoning about proteolytic events.CleavPredict is freely accessible, and there is no login required.

View Article: PubMed Central - PubMed

Affiliation: Sanford Burnham Medical Research Institute, La Jolla, California, United States of America.

ABSTRACT
CleavPredict (http://cleavpredict.sanfordburnham.org) is a Web server for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers in silico prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results. To augment the substrate cleavage prediction process, CleavPredict provides information about the structural features of potential cleavage sites that influence proteolysis. These include: secondary structure, disordered regions, transmembrane domains, and solvent accessibility. The server also provides information about subcellular location, co-localization, and co-expression of proteinase and potential substrates, along with experimentally determined positions of single nucleotide polymorphism (SNP), and posttranslational modification (PTM) sites in substrates. All this information will provide the user with perspectives in reasoning about proteolytic events. CleavPredict is freely accessible, and there is no login required.

No MeSH data available.


Related in: MedlinePlus

Distribution of PWM scores for peptide substrates of MMP-2 from Schilling et al. [66].Red line—distribution of PWM score values for experimentally identified cleaved peptide bonds, black line—distribution of scores for all other peptide bonds. Red—dashed line represents distribution of scores for set of cleaved peptide bonds corrected by replacing poorly scored peptide bonds by those that have their scores above the threshold and were located in the vicinity of experimentally predicted positions. The separation between the cleavage site scores and the scores for other peptide bonds was subject to Kolmogorov-Smirnov test yielding D = 0.60 and D = 0.66 for red and red-dashed distributions, respectively, when tested against the black one.
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pone.0127877.g001: Distribution of PWM scores for peptide substrates of MMP-2 from Schilling et al. [66].Red line—distribution of PWM score values for experimentally identified cleaved peptide bonds, black line—distribution of scores for all other peptide bonds. Red—dashed line represents distribution of scores for set of cleaved peptide bonds corrected by replacing poorly scored peptide bonds by those that have their scores above the threshold and were located in the vicinity of experimentally predicted positions. The separation between the cleavage site scores and the scores for other peptide bonds was subject to Kolmogorov-Smirnov test yielding D = 0.60 and D = 0.66 for red and red-dashed distributions, respectively, when tested against the black one.

Mentions: We applied our prediction method to all reported peptides. The experimentally identified cleavage sites were considered to be a positive set while all other peptides bonds were negative set. We used CleavPredict to evaluate all peptide bonds in substrates and calculated the distribution of PWM score values for the positive and negative sets. The results are presented in Figs 1 and 2. In each case the separation between the scores for negative and positive sets is significant. In the two-sample Kolmogorov-Smirnov (KS) test the value of D statistic is equal to 0.6.


CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events.

Kumar S, Ratnikov BI, Kazanov MD, Smith JW, Cieplak P - PLoS ONE (2015)

Distribution of PWM scores for peptide substrates of MMP-2 from Schilling et al. [66].Red line—distribution of PWM score values for experimentally identified cleaved peptide bonds, black line—distribution of scores for all other peptide bonds. Red—dashed line represents distribution of scores for set of cleaved peptide bonds corrected by replacing poorly scored peptide bonds by those that have their scores above the threshold and were located in the vicinity of experimentally predicted positions. The separation between the cleavage site scores and the scores for other peptide bonds was subject to Kolmogorov-Smirnov test yielding D = 0.60 and D = 0.66 for red and red-dashed distributions, respectively, when tested against the black one.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4440711&req=5

pone.0127877.g001: Distribution of PWM scores for peptide substrates of MMP-2 from Schilling et al. [66].Red line—distribution of PWM score values for experimentally identified cleaved peptide bonds, black line—distribution of scores for all other peptide bonds. Red—dashed line represents distribution of scores for set of cleaved peptide bonds corrected by replacing poorly scored peptide bonds by those that have their scores above the threshold and were located in the vicinity of experimentally predicted positions. The separation between the cleavage site scores and the scores for other peptide bonds was subject to Kolmogorov-Smirnov test yielding D = 0.60 and D = 0.66 for red and red-dashed distributions, respectively, when tested against the black one.
Mentions: We applied our prediction method to all reported peptides. The experimentally identified cleavage sites were considered to be a positive set while all other peptides bonds were negative set. We used CleavPredict to evaluate all peptide bonds in substrates and calculated the distribution of PWM score values for the positive and negative sets. The results are presented in Figs 1 and 2. In each case the separation between the scores for negative and positive sets is significant. In the two-sample Kolmogorov-Smirnov (KS) test the value of D statistic is equal to 0.6.

Bottom Line: The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results.All this information will provide the user with perspectives in reasoning about proteolytic events.CleavPredict is freely accessible, and there is no login required.

View Article: PubMed Central - PubMed

Affiliation: Sanford Burnham Medical Research Institute, La Jolla, California, United States of America.

ABSTRACT
CleavPredict (http://cleavpredict.sanfordburnham.org) is a Web server for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers in silico prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results. To augment the substrate cleavage prediction process, CleavPredict provides information about the structural features of potential cleavage sites that influence proteolysis. These include: secondary structure, disordered regions, transmembrane domains, and solvent accessibility. The server also provides information about subcellular location, co-localization, and co-expression of proteinase and potential substrates, along with experimentally determined positions of single nucleotide polymorphism (SNP), and posttranslational modification (PTM) sites in substrates. All this information will provide the user with perspectives in reasoning about proteolytic events. CleavPredict is freely accessible, and there is no login required.

No MeSH data available.


Related in: MedlinePlus