ArticleGenomics, proteomics & bioinformatics2020
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.
Article in Genomics, proteomics & bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
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Who cites it
71 citing papers in PubMed, 1 synthesis or guideline pooled it, 145 citations in OpenAlex.
- Iron dysregulation in COVID-19 and reciprocal evolution of SARS-CoV-2: Natura nihil frustra facit.Journal of cellular biochemistry · 2022Pooled it
- PhageScout: Protease Cleavage Site Prediction Using an Experimental Substrate Phage Display Motif-Based Approach.International journal of molecular sciences · 2026Article
- Predicting intracranial hypertension as a secondary insult using the pathological peptidome of brain injured patients.Scientific reports · 2026Article
- Preparation and Identification of Corn-Derived Bioactive Peptides with Triple Efficacy of ADH-Activating, XOD-Inhibiting and Antioxidant Activity.Foods (Basel, Switzerland) · 2026Article
- A High-Coverage Epitope-Based Vaccine Design for EIAV Envelope Polyprotein Using an Immunoinformatic Approach.Veterinary sciences · 2026Article
- The rise and future of peptide-based antimicrobials.Journal of microbiology (Seoul, Korea) · 2026Review
- Unbiased cleavage site prediction uncovers viral antagonism of host innate immunity by SARS-CoV-2 3C-like protease.JCI insight · 2026Article
- Improved antioxidant and anti-melanogenic effects of ovalbumin derived from egg white after enzymatic hydrolysis.Food science of animal resources · 2026Article
- Deep learning guided design of protease substrates.Nature communications · 2026Article
- Lab to codes: multimodel advanced AI-driven pipelines to drive antimicrobial peptide design for the post-antibiotic era.Frontiers in cellular and infection microbiology · 2026Review
- Implementing N-terminomics and machine learning to probe Nt-arginylation.Nature communications · 2025Article
- Leveraging artificial intelligence in antibody-drug conjugate development: from target identification to clinical translation in oncology.NPJ precision oncology · 2025Review
- Data Processing and Analysis in Positional Proteomics.Proteomics · 2025Review
- High-Throughput Activity Reprogramming of Proteases (HARP).ACS chemical biology · 2025Article
- Profiling plasma protease activity with charge-changing peptides enables detection and classification of gastrointestinal cancers.Scientific reports · 2025Article
- A game of tag: A review of protein tags for the successful detection, purification and fluorescence labelling of proteins expressed in microalgae.The Plant journal : for cell and molecular biology · 2025Review
- Apoptotic Caspases-3 and -7 Cleave Extracellular Domains of Membrane-Bound Proteins from MDA-MB-231 Breast Cancer Cells.International journal of molecular sciences · 2025Article
- PredLyP: A computational tool for predicting tissue-specific (phago-)lysosomal post-digestion peptides.Computational and structural biotechnology journal · 2025Article
- Investigating Protein-Protein Interactions of Autophagy-Involved TNIP1.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Fibroblast-like synoviocytes mediate the generation of soluble PD-1 in an MMP-9-dependent manner: a novel target therapy for rheumatoid arthritis.Frontiers in immunology · 2025Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 4 countries.
Funding
Abstract
Proteases are enzymes that cleave and hydrolyse the peptide bonds between two specific amino acid residues of target substrate proteins. Protease-controlled proteolysis plays a key role in the degradation and recycling of proteins, which is essential for various physiological processes. Thus, solving the substrate identification problem will have important implications for the precise understanding of functions and physiological roles of proteases, as well as for therapeutic target identification and pharmaceutical applicability. Consequently, there is a great demand for bioinformatics methods that can predict novel substrate cleavage events with high accuracy by utilizing both sequence and structural information. In this study, we present Procleave, a novel bioinformatics approach for predicting protease-specific substrates and specific cleavage sites by taking into account both their sequence and 3D structural information. Structural features of known cleavage sites were represented by discrete values using a LOWESS data-smoothing optimization method, which turned out to be critical for the performance of Procleave. The optimal approximations of all structural parameter values were encoded in a conditional random field (CRF) computational framework, alongside sequence and chemical group-based features. Here, we demonstrate the outstanding performance of Procleave through extensive benchmarking and independent tests. Procleave is capable of correctly identifying most cleavage sites in the case study. Importantly, when applied to the human structural proteome encompassing 17,628 protein structures, Procleave suggests a number of potential novel target substrates and their corresponding cleavage sites of different proteases. Procleave is implemented as a webserver and is freely accessible at http://procleave.erc.monash.edu/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.