AIMC Topic: Catalytic Domain

Clear Filters Showing 31 to 40 of 43 articles

A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes.

Scientific reports Nov 13, 2018
Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approaches have fac...
Stereoisomerism Substrate Specificity Directed Molecular Evolution Epoxide Hydrolases Models, Molecular Mutation Aspergillus niger Catalytic Domain Machine Learning
View on PubMed DOI

Integration of virtual screening and susceptibility test to discover active-site subpocket-specific biogenic inhibitors of Helicobacter pylori shikimate dehydrogenase.

International microbiology : the official journal of the Spanish Society for Microbiology Aug 24, 2018
Shikimate dehydrogenase (HpSDH) (EC 1.1.1.25) is a key enzyme in the shikimate pathway of Helicobacter pylori (H. pylori), which catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. Targeting HpSDH has been recognize...
Catalytic Domain Alcohol Oxidoreductases Crystallography, X-Ray Protein Conformation Computational Biology Helicobacter pylori Drug Evaluation, Preclinical Enzyme Inhibitors Anti-Bacterial Agents Molecular Docking Simulation Microbial Sensitivity Tests
View on PubMed DOI

Design, synthesis, antibacterial evaluation and molecular docking studies of some new quinoxaline derivatives targeting dihyropteroate synthase enzyme.

Bioorganic chemistry Dec 5, 2017
Development of new antimicrobial agents is a good solution to overcome drug-resistance problems. From this perspective, new quinoxaline derivatives bearing various bioactive heterocyclic moieties (thiadiazoles, oxadiazoles, pyrazoles and thiazoles) w...
Catalytic Domain Gram-Negative Bacteria Gram-Positive Bacteria Hydrogen Bonding Protein Binding Structure-Activity Relationship Molecular Structure Hydrophobic and Hydrophilic Interactions Dihydropteroate Synthase Quinoxalines Levofloxacin Yersinia pestis Anti-Bacterial Agents Molecular Docking Simulation Drug Design Microbial Sensitivity Tests
View on PubMed DOI

In silico identification of milk antihypertensive di- and tripeptides involved in angiotensin I-converting enzyme inhibitory activity.

Nutrition research (New York, N.Y.) Jul 28, 2017
Identification of bioactive milk peptides could improve food technology through improved selection of food supplements with a focus on antihypertensive properties. We hypothesized that angiotensin I-converting enzyme (ACE) inhibitory activities of mi...
Cattle Computational Biology Dietary Supplements Antihypertensive Agents Humans Animals Molecular Docking Simulation Quantitative Structure-Activity Relationship Protein Conformation Hydrogen Bonding Peptidyl-Dipeptidase A Proteolysis Binding Sites Milk Proteins Expert Systems Catalytic Domain Oligopeptides Angiotensin-Converting Enzyme Inhibitors Models, Molecular Peptide Fragments Dipeptides Hydrophobic and Hydrophilic Interactions
View on PubMed DOI

Discriminating between HuR and TTP binding sites using the k-spectrum kernel method.

PloS one Mar 23, 2017
BACKGROUND: The RNA binding proteins (RBPs) human antigen R (HuR) and Tristetraprolin (TTP) are known to exhibit competitive binding but have opposing effects on the bound messenger RNA (mRNA). How cells discriminate between the two proteins is an in...
Catalytic Domain Binding Sites ELAV-Like Protein 1 Tristetraprolin Humans Models, Theoretical Support Vector Machine
View on PubMed DOI

Classifying kinase conformations using a machine learning approach.

BMC bioinformatics Feb 2, 2017
BACKGROUND: Signaling proteins such as protein kinases adopt a diverse array of conformations to respond to regulatory signals in signaling pathways. Perhaps the most fundamental conformational change of a kinase is the transition between active and ...
Machine Learning Models, Molecular Protein Kinases Catalytic Domain Protein Conformation
View on PubMed DOI

Synthesis and antimicrobial studies of novel derivatives of 4-(4-formyl-3-phenyl-1H-pyrazol-1-yl)benzoic acid as potent anti-Acinetobacter baumannii agents.

Bioorganic & medicinal chemistry letters Dec 29, 2016
Microbial resistance to antibiotics is a global concern. The World Health Organization (WHO) has identified antimicrobial resistance as one the three greatest threats for human beings in the 21st century. Without urgent and coordinated action, the wo...
Pyrazoles Gram-Negative Bacteria Gram-Positive Bacteria Binding Sites Structure-Activity Relationship Catalytic Domain Acinetobacter baumannii Benzoic Acid Anti-Infective Agents Molecular Docking Simulation Microbial Sensitivity Tests Drug Resistance, Multiple, Bacterial
View on PubMed DOI

Development of 3D-QSAR Model for Acetylcholinesterase Inhibitors Using a Combination of Fingerprint, Molecular Docking, and Structure-Based Pharmacophore Approaches.

Toxicological sciences : an official journal of the Society of Toxicology Jul 21, 2015
Acetylcholinesterase (AChE), a serine hydrolase vital for regulating the neurotransmitter acetylcholine in animals, has been used as a target for drugs and pesticides. With the increasing availability of AChE crystal structures, with or without ligan...
Molecular Conformation Quantitative Structure-Activity Relationship Binding Sites Peptide Mapping Nootropic Agents Acetylcholinesterase Cholinesterase Inhibitors Expert Systems Catalytic Domain Models, Molecular GPI-Linked Proteins Insecticides Ligands Humans Artificial Intelligence Animals Molecular Docking Simulation Imaging, Three-Dimensional Computational Biology Databases, Protein Nerve Tissue Proteins
View on PubMed DOI

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 Protein Binding Structure-Activity Relationship Molecular Structure Quantum Theory Arachidonate 5-Lipoxygenase Cyclooxygenase 2 Lipoxygenase Inhibitors Substrate Specificity Ligands Cyclooxygenase 2 Inhibitors Datasets as Topic Catalytic Domain
View on PubMed DOI

SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations.

Genomics, proteomics & bioinformatics Jan 15, 2025
The accurate identification of catalytic residues contributes to our understanding of enzyme functions in biological processes and pathways. The increasing number of protein sequences necessitates computational tools for the automated prediction of c...
Computational Biology Mutation Catalytic Domain Enzymes Humans Neural Networks, Computer Machine Learning Software
View on PubMed DOI
Popular Topics
Recent Journals