AIMC Topic: Substrate Specificity
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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...
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...
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...
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...
Lipoxygenase Inhibitors
Substrate Specificity
Arachidonate 5-Lipoxygenase
Cyclooxygenase 2
Molecular Structure
Humans
Quantum Theory
Ligands
Cyclooxygenase 2 Inhibitors
Molecular Docking Simulation
Datasets as Topic
Protein Binding
Catalytic Domain
Structure-Activity Relationship
Neural Networks, Computer
Algorithms
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...
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...
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...
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...
Catalytic mechanism and engineering of aromatic prenyltransferase: A review.
International journal of biological macromolecules
Jun 1, 2025
The prenylation of aromatic compounds significantly enhances their metabolic stability and bioactivity. Prenyltransferases, as essential biocatalysts, facilitate the regioselective transfer of prenyl groups from donors to aromatic substrates. This re...
CHCHD4 Oxidoreductase Activity: A Comprehensive Analysis of the Molecular, Functional, and Structural Properties of Its Redox-Regulated Substrates.
Molecules (Basel, Switzerland)
May 10, 2025
The human CHCHD4 protein, which is a prototypical family member, carries a coiled-coil-helix-coiled-coil-helix motif that is stabilized by two disulfide bonds. Using its CPC sequence motif, CHCHD4 plays a key role in mitochondrial metabolism, cell su...
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