AIMC Topic: Substrate Specificity

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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...
Machine Learning Peptides Ligands Protease Inhibitors Protein Conformation Small Molecule Libraries Substrate Specificity Peptide Hydrolases User-Computer Interface Databases, Pharmaceutical Models, Molecular Drug Evaluation, Preclinical
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Development of a Support Vector Machine-Based System to Predict Whether a Compound Is a Substrate of a Given Drug Transporter Using Its Chemical Structure.

Journal of pharmaceutical sciences Jun 1, 2016
The aim of this study was to develop an in silico prediction system to assess which of 7 categories of drug transporters (organic anion transporting polypeptide [OATP] 1B1/1B3, multidrug resistance-associated protein [MRP] 2/3/4, organic anion transp...
Lipids Predictive Value of Tests Pharmaceutical Preparations Computer Simulation Support Vector Machine Carrier Proteins Multidrug Resistance-Associated Proteins Biological Transport Molecular Weight Substrate Specificity Algorithms
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A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs.

BMC bioinformatics Dec 9, 2015
Protein O-GlcNAcylation, involving the β-attachment of single N-acetylglucosamine (GlcNAc) to the hydroxyl group of serine or threonine residues, is an O-linked glycosylation catalyzed by O-GlcNAc transferase (OGT). Molecular level investigation of t...
Support Vector Machine Peptides Proteins Machine Learning Mass Spectrometry Amino Acid Motifs Algorithms Acetylglucosamine User-Computer Interface N-Acetylglucosaminyltransferases Internet Glycosylation Substrate Specificity
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Prediction the Substrate Specificities of Membrane Transport Proteins Based on Support Vector Machine and Hybrid Features.

IEEE/ACM transactions on computational biology and bioinformatics Nov 11, 2015
Membrane transport proteins and their substrate specificities play crucial roles in a variety of cellular functions. Identifying the substrate specificities of membrane transport proteins is closely related to the protein-target interaction predictio...
Membrane Transport Proteins Binding Sites Substrate Specificity Protein Interaction Mapping Sequence Analysis, Protein Support Vector Machine Models, Chemical Pattern Recognition, Automated Algorithms Molecular Docking Simulation Protein Binding
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Purification and biochemical properties of SDS-stable low molecular weight alkaline serine protease from Citrullus colocynthis.

Natural product research Sep 1, 2015
A low molecular weight serine protease from seeds of Citrullus colocynthis was purified to electrophoretic homogeneity with high level of catalytic efficiency (22,945 M(-1) S(-1)). The enzyme was a monomer with molecular mass of 25 kDa estimated by S...
Citrullus colocynthis Hydrogen-Ion Concentration Serine Proteases Temperature Molecular Weight Electrophoresis, Polyacrylamide Gel Seeds Enzyme Stability Substrate Specificity
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The study of dual COX-2/5-LOX inhibitors by using electronic-topological approach based on data on the ligand-receptor interactions.

Journal of molecular graphics & modelling Jun 19, 2015
Structural and electronic factors influencing selective inhibition of cyclooxygenase-2 and 5-lipoxygenase (COX-2/5-LOX) were studied by using Electronic-Topological Method combined with Neural Networks (ETM-NN), molecular docking, and Density Functio...
Humans Neural Networks, Computer Algorithms Molecular Docking Simulation Datasets as Topic Quantum Theory Cyclooxygenase 2 Catalytic Domain Protein Binding Ligands Lipoxygenase Inhibitors Cyclooxygenase 2 Inhibitors Structure-Activity Relationship Arachidonate 5-Lipoxygenase Substrate Specificity Molecular Structure
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MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Nature methods May 4, 2015
Protein phosphorylation is important in cellular pathways and altered in disease. We developed MIMP (http://mimp.baderlab.org/), a machine learning method to predict the impact of missense single-nucleotide variants (SNVs) on kinase-substrate interac...
Mutation, Missense Artificial Intelligence Phosphotransferases Phosphorylation Amino Acid Sequence Software Substrate Specificity Polymorphism, Single Nucleotide Signal Transduction
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Engineering catalytically promiscuous enzymes to serve new functions.

Biotechnology advances Sep 1, 2025
Catalytic promiscuity in enzymes refers to their ability to catalyze multiple chemically distinct reactions in addition to their native activity. The increasing discovery of additional enzymes exhibiting catalytic promiscuity has underscored the sign...
Catalysis Biocatalysis Substrate Specificity Protein Engineering Enzymes
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Protease engineering: Approaches, tools, and emerging trends.

Biotechnology advances Sep 1, 2025
Engineered proteases with bespoke substrate specificities and activities can empower broad and innovative applications in biomedicine, mass spectrometry-based proteomics, and chemical and synthetic biology. This review provides an authoritative, topi...
Directed Molecular Evolution Protein Engineering Peptide Hydrolases Humans Substrate Specificity
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Assessing Substrate Scope of the Cyclodehydratase LynD by mRNA Display-Enabled Machine Learning Models.

Biochemistry Jul 1, 2025
Many members of the broad family of enzymes, known as YcaOs have been shown to install azoline heterocycles post-translationally into peptide substrates. These moieties can help rigidify structures and contribute to the potent bioactivities of the ev...
Peptides RNA, Messenger Substrate Specificity Machine Learning
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