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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.


Snapshots of the result pages.As an example the prediction of the cleavage positions in Q15848 protein for MMP2 enzyme is demonstrated. This section contains information about signal peptide prediction, subcellular location, co-expression and co-localization information, known cleavages in CutDB, data on experimentally identified SNPs and PTMs, congregated into tables.
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pone.0127877.g005: Snapshots of the result pages.As an example the prediction of the cleavage positions in Q15848 protein for MMP2 enzyme is demonstrated. This section contains information about signal peptide prediction, subcellular location, co-expression and co-localization information, known cleavages in CutDB, data on experimentally identified SNPs and PTMs, congregated into tables.

Mentions: The two sections/tiers of the output data are summarized in Fig 4. All the results are shown in tabular form (see example in Fig 5). The form of the first section of the output depends on the type of input query. When a query input is in the form of a protein sequence, then the first table contains a list of predicted P1 cleavage positions, 10 amino acid sequences around the cleavage site, a PWM score, the predicted secondary structure (alphahelix; ‘H’, beta-sheet; ‘E’. loop; ‘_’) and the predicted disorder (order: ‘.’; disorder ‘*’) characterizing this region of 10 amino acids. In addition, for each of these 10 amino acid positions, the server reports confidence scores of prediction in the range of 0–9, calculated by the Jnet and the Disopred programs. The confidence score is computed for every amino acid position, as a separate number. Thus, for ten amino acids fragment the server reports ten numbers in the form of a chain of consecutive values. The table also provides information about the presence of transmembrane domain for 10 amino acids region around the cleavage site, as predicted by the TMHMM program; and N-terminal and C-terminal mass fragments resultant from each cleavage event (Fig 5, label: A).


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

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

Snapshots of the result pages.As an example the prediction of the cleavage positions in Q15848 protein for MMP2 enzyme is demonstrated. This section contains information about signal peptide prediction, subcellular location, co-expression and co-localization information, known cleavages in CutDB, data on experimentally identified SNPs and PTMs, congregated into tables.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0127877.g005: Snapshots of the result pages.As an example the prediction of the cleavage positions in Q15848 protein for MMP2 enzyme is demonstrated. This section contains information about signal peptide prediction, subcellular location, co-expression and co-localization information, known cleavages in CutDB, data on experimentally identified SNPs and PTMs, congregated into tables.
Mentions: The two sections/tiers of the output data are summarized in Fig 4. All the results are shown in tabular form (see example in Fig 5). The form of the first section of the output depends on the type of input query. When a query input is in the form of a protein sequence, then the first table contains a list of predicted P1 cleavage positions, 10 amino acid sequences around the cleavage site, a PWM score, the predicted secondary structure (alphahelix; ‘H’, beta-sheet; ‘E’. loop; ‘_’) and the predicted disorder (order: ‘.’; disorder ‘*’) characterizing this region of 10 amino acids. In addition, for each of these 10 amino acid positions, the server reports confidence scores of prediction in the range of 0–9, calculated by the Jnet and the Disopred programs. The confidence score is computed for every amino acid position, as a separate number. Thus, for ten amino acids fragment the server reports ten numbers in the form of a chain of consecutive values. The table also provides information about the presence of transmembrane domain for 10 amino acids region around the cleavage site, as predicted by the TMHMM program; and N-terminal and C-terminal mass fragments resultant from each cleavage event (Fig 5, label: A).

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.