ArticlePLoS computational biology2013
Cleavage entropy as quantitative measure of protease specificity.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Deep learning guided design of protease substrates.Nature communications · 2026Article
- Temporal interference stimulation of peripheral nerves induces functionally diverse limb movements revealed by automated pose estimation and unsupervised behavioral analysis.Journal of neuroengineering and rehabilitation · 2025Article
- Identification of pancreatic cancer-specific protease substrates for protease-dependent targeted delivery.Oncogenesis · 2024Article
- Predicting Structural Susceptibility of Proteins to Proteolytic Processing.International journal of molecular sciences · 2023Article
- PepFun: Open Source Protocols for Peptide-Related Computational Analysis.Molecules (Basel, Switzerland) · 2021Article
- Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen.Nature communications · 2021Article
- Quantitative profiling of protease specificity.PLoS computational biology · 2021Article
- An automated protocol for modelling peptide substrates to proteases.BMC bioinformatics · 2020Article
- Enhancing the promiscuity of a member of the Caspase protease family by rational design.Proteins · 2020Article
- Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.Briefings in bioinformatics · 2019Review
- Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces.Journal of chemical theory and computation · 2019Article
- Predictive models of protease specificity based on quantitative protease-activity profiling data.Biochimica et biophysica acta. Proteins and proteomics · 2019Article
- An unexpected switch in peptide binding mode: from simulation to substrate specificity.Journal of biomolecular structure & dynamics · 2018Article
- Electrostatic recognition in substrate binding to serine proteases.Journal of molecular recognition : JMR · 2018Article
- Dissecting Substrate Specificities of the Mitochondrial AFG3L2 Protease.Biochemistry · 2018Article
- Phage-assisted continuous evolution of proteases with altered substrate specificity.Nature communications · 2017Article
- Block-based characterization of protease specificity from substrate sequence profile.BMC bioinformatics · 2017Article
- Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.Scientific reports · 2017Article
- 3D proteochemometrics: using three-dimensional information of proteins and ligands to address aspects of the selectivity of serine proteases.MedChemComm · 2017Article
- Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data.Current protein & peptide science · 2017Review
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7 authors.
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Abstract
A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity.
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