AIMC Topic: Peptide Hydrolases

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Predicting Proteolysis in Complex Proteomes Using Deep Learning.

International journal of molecular sciences Mar 17, 2021
Both protease- and reactive oxygen species (ROS)-mediated proteolysis are thought to be key effectors of tissue remodeling. We have previously shown that comparison of amino acid composition can predict the differential susceptibilities of proteins t...
Proteolysis Peptide Hydrolases Extracellular Matrix Proteins Software Reproducibility of Results Deep Learning Amino Acids Humans Proteome Ultraviolet Rays Neural Networks, Computer Reactive Oxygen Species
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Deep learning model for virtual screening of novel 3C-like protease enzyme inhibitors against SARS coronavirus diseases.

Computers in biology and medicine Mar 6, 2021
In the context of the recently emerging COVID-19 pandemic, we developed a deep learning model that can be used to predict the inhibitory activity of 3CLpro in severe acute respiratory syndrome coronavirus (SARS-CoV) for unknown compounds during the v...
Humans Pandemics COVID-19 Molecular Docking Simulation Bayes Theorem Deep Learning SARS-CoV-2 Protease Inhibitors Antiviral Agents Peptide Hydrolases Severe acute respiratory syndrome-related coronavirus
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New machine learning and physics-based scoring functions for drug discovery.

Scientific reports Feb 4, 2021
Scoring functions are essential for modern in silico drug discovery. However, the accurate prediction of binding affinity by scoring functions remains a challenging task. The performance of scoring functions is very heterogeneous across different tar...
Humans Software Research Design Internet Ligands Hydrophobic and Hydrophilic Interactions Datasets as Topic Molecular Docking Simulation Drug Discovery Support Vector Machine Protein Interaction Mapping Drugs, Investigational Protease Inhibitors Peptide Hydrolases Entropy
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Noninvasive diagnostic of periprosthetic joint infection by urinary peptide markers: A preliminary study.

Journal of orthopaedic research : official publication of the Orthopaedic Research Society Nov 25, 2020
Previous immunohistochemical analyses revealed altered protein expression in the periprosthetic membranes of patients with periprosthetic joint infection (PJI). Proteins are degraded to peptides that may pass the blood-kidney barrier depending on the...
Sequence Analysis, Protein Support Vector Machine Peptide Hydrolases Prosthesis-Related Infections Humans Peptides Proteome Biomarkers Aged
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Highly Stable Passive Wireless Sensor for Protease Activity Based on Fatty Acid-Coupled Gelatin Composite Films.

Analytical chemistry Sep 14, 2020
Proteases are often used as biomarkers of many pathologies as well as of microbial contamination and infection. Therefore, extensive efforts are devoted to the development of protease sensors. Some applications would benefit from wireless monitoring ...
Gelatin Wireless Technology Aspergillus Fatty Acids Quartz Crystal Microbalance Techniques Peptide Hydrolases Support Vector Machine
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Predictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease.

Journal of biomolecular structure & dynamics Aug 5, 2020
The whole world is facing a great challenging time due to Coronavirus disease (COVID-19) caused by SARS-CoV-2. Globally, more than 14.6 M people have been diagnosed and more than 595 K deaths are reported. Currently, no effective vaccine or drugs are...
Humans Protease Inhibitors COVID-19 Peptide Hydrolases Deep Learning Molecular Dynamics Simulation SARS-CoV-2 Molecular Docking Simulation
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Identification of Methylated Gene Biomarkers in Patients with Alzheimer's Disease Based on Machine Learning.

BioMed research international Mar 26, 2020
BACKGROUND: Alzheimer's disease (AD) is a neurodegenerative disorder and characterized by the cognitive impairments. It is essential to identify potential gene biomarkers for AD pathology.
Humans Machine Learning Gene Expression Regulation, Neoplastic Carrier Proteins DNA-Binding Proteins Transcription Factors DNA Methylation Protein Tyrosine Phosphatases Peptide Hydrolases Genetic Markers Mitochondrial Proteins Microfilament Proteins Alzheimer Disease Patients Cyclin-Dependent Kinase Inhibitor p57
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Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations.

Proceedings of the National Academy of Sciences of the United States of America Dec 26, 2018
Biophysical interactions between proteins and peptides are key determinants of molecular recognition specificity landscapes. However, an understanding of how molecular structure and residue-level energetics at protein-peptide interfaces shape these l...
Serine Proteases Viral Nonstructural Proteins Substrate Specificity Peptide Hydrolases High-Throughput Nucleotide Sequencing Energy Metabolism Structure-Activity Relationship Drug Resistance, Viral Antiviral Agents Models, Molecular Supervised Machine Learning Metabolomics Hepacivirus
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Unveiling antimicrobial peptide-generating human proteases using PROTEASIX.

Journal of proteomics Feb 27, 2017
UNLABELLED: Extracting information from peptidomics data is a major current challenge, as endogenous peptides can result from the activity of multiple enzymes. Proteolytic enzymes can display overlapping or complementary specificity. The activity spe...
Peptides Peptide Hydrolases Antimicrobial Cationic Peptides Protein Precursors Humans Computational Biology Knowledge Bases Substrate Specificity Proteome
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Protease Inhibitors in View of Peptide Substrate Databases.

Journal of chemical information and modeling Jun 9, 2016
Protease substrate profiling has nowadays almost become a routine task for experimentalists, and the knowledge on protease peptide substrates is easily accessible via the MEROPS database. We present a shape-based virtual screening workflow using vROC...
Protein Conformation Substrate Specificity Protease Inhibitors Databases, Pharmaceutical Small Molecule Libraries Machine Learning Models, Molecular Peptide Hydrolases Peptides Drug Evaluation, Preclinical User-Computer Interface Ligands
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