AIMC Topic: Protein Kinases

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Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges.

Journal of computer-aided molecular design Aug 16, 2018
Advanced mathematics, such as multiscale weighted colored subgraph and element specific persistent homology, and machine learning including deep neural networks were integrated to construct mathematical deep learning models for pose and binding affin...
Crystallography, X-Ray Protein Conformation Receptors, Cytoplasmic and Nuclear Protein Kinases Ligands Thermodynamics Cathepsins Binding Sites Computer-Aided Design Drug Design Protein Binding Databases, Protein Deep Learning Molecular Docking Simulation
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Redefining the Protein Kinase Conformational Space with Machine Learning.

Cell chemical biology May 31, 2018
Protein kinases are dynamic, adopting different conformational states that are critical for their catalytic activity. We assess a range of structural features derived from the conserved αC helix and DFG motif to define the conformational space of the...
Machine Learning Models, Molecular Protein Kinases Humans Protein Kinase Inhibitors Small Molecule Libraries Ligands Protein Conformation
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Assisting document triage for human kinome curation via machine learning.

Database : the journal of biological databases and curation Jan 1, 2018
In the era of data explosion, the increasing frequency of published articles presents unorthodox challenges to fulfill specific curation requirements for bio-literature databases. Recognizing these demands, we designed a document triage system with a...
Protein Kinases Data Mining Documentation Machine Learning Proteome Statistics as Topic Humans
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Novel Method Proposing Chemical Structures with Desirable Profile of Activities Based on Chemical and Protein Spaces.

Molecular informatics Aug 30, 2017
Active molecules among numerous chemical structures in a chemical database can be searched easily by statistical prediction of compound-protein interactions. However, constructing a simple prediction model against one protein does not aid drug design...
Neural Networks, Computer Drug Design Databases, Chemical Protein Kinases Humans
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Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates.

Molecular & cellular proteomics : MCP Mar 6, 2017
Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts of cellular material. Despite this wealth of information, our understanding of phosphorylation-based signaling is limited, in part because it is...
Substrate Specificity Saccharomyces cerevisiae Proteins Saccharomyces cerevisiae Pyrimidines Phosphorylation Phosphoproteins DNA Mutational Analysis Pyrazoles Protein Kinases Machine Learning Algorithms Proteomics
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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 ...
Models, Molecular Protein Kinases Machine Learning Catalytic Domain Protein Conformation
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Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries.

Journal of chemical information and modeling May 24, 2016
Virtual screening consists of docking libraries of small molecules to a target protein followed by rank-ordering of the resulting structures using scoring functions. The ability of scoring methods to distinguish between actives and inactives depends ...
Crystallography, X-Ray Small Molecule Libraries Drug Evaluation, Preclinical Protein Kinases Ligands Protein Binding Support Vector Machine Molecular Docking Simulation User-Computer Interface
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Sensitive and versatile electrogenerated chemiluminescence biosensing platform for protein kinase based on Ru(bpy)3(2+) functionalized gold nanoparticles mediated signal transduction.

Analytica chimica acta Dec 17, 2015
A novel, sensitive and versatile electrogenerated chemiluminescence biosensing platform is developed for monitoring activity and inhibition of protein kinase based on Ru(bpy)3(2+) functionalized gold nanoparticles (Ru(bpy)3(2+)-AuNPs) mediated signal...
Luminescence Protein Kinases Ruthenium Compounds Microscopy, Atomic Force Signal Transduction Gold Metal Nanoparticles Sensitivity and Specificity Biosensing Techniques
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Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor.

BMC bioinformatics Sep 18, 2015
BACKGROUND: Two component systems (TCS) are signalling complexes manifested by a histidine kinase (receptor) and a response regulator (effector). They are the most abundant signalling pathways in prokaryotes and control a wide range of biological pro...
Support Vector Machine Area Under Curve Bacterial Proteins Protein Interaction Maps Bacteria Histidine Kinase Protein Kinases Genome, Bacterial ROC Curve
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A Pretrained ELECTRA Model for Kinase-Specific Phosphorylation Site Prediction.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2022
Phosphorylation plays a vital role in signal transduction and cell cycle. Identifying and understanding phosphorylation through machine-learning methods has a long history. However, existing methods only learn representations of a protein sequence se...
Machine Learning Phosphorylation Protein Kinases
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