AI Medical Compendium Topic:
Protein Binding

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Machine Learning Models for Accurate Prediction of Kinase Inhibitors with Different Binding Modes.

Journal of medicinal chemistry Aug 30, 2019
Noncovalent inhibitors of protein kinases have different modes of action. They bind to the active or inactive form of kinases, compete with ATP, stabilize inactive kinase conformations, or act through allosteric sites. Accordingly, kinase inhibitors ...
Protein Binding Protein Kinases Datasets as Topic Databases, Chemical Crystallography, X-Ray Protein Kinase Inhibitors Machine Learning
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Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships.

Journal of computer-aided molecular design Aug 21, 2019
In this work, computational compound screening strategies on the basis of two- and three-dimensional (2D and 3D) molecular representations were investigated including similarity searching and support vector machine (SVM) ranking. Calculations based o...
Structure-Activity Relationship Molecular Conformation Computational Chemistry User-Computer Interface Protein Binding Support Vector Machine Machine Learning
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Target-Specific Prediction of Ligand Affinity with Structure-Based Interaction Fingerprints.

Journal of chemical information and modeling Aug 19, 2019
Discovery and optimization of small molecule inhibitors as therapeutic drugs have immensely benefited from rational structure-based drug design. With recent advances in high-resolution structure determination, computational power, and machine learnin...
Humans Machine Learning Molecular Docking Simulation HIV-1 Drug Design Ligands Drug Discovery HIV Protease HIV Infections HIV Protease Inhibitors Protein Binding
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Artificial Intelligence Approach To Investigate the Longevity Drug.

The journal of physical chemistry letters Aug 14, 2019
Longevity is a very important and interesting topic, and has been demonstrated to be related to longevity. We combined network pharmacology, machine learning, deep learning, and molecular dynamics (MD) simulation to investigate potent lead drugs. Re...
Artificial Intelligence Protein Interaction Maps Protein Binding Signal Transduction Medicine, Chinese Traditional Algorithms Databases, Factual Molecular Docking Simulation Drug Discovery Thermodynamics Receptor, Insulin Klotho Proteins Glucuronidase Receptor, IGF Type 1 Antigens, CD Ligands Inhibitory Concentration 50 Binding Sites
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BindSpace decodes transcription factor binding signals by large-scale sequence embedding.

Nature methods Aug 12, 2019
The decoding of transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF labels into the same space. By training on binding data f...
Chromatin Immunoprecipitation Transcription Factors DNA Binding Sites Humans Machine Learning Algorithms Protein Binding Computational Biology
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Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response.

BMC biology Jul 30, 2019
BACKGROUND: Identification of functional non-coding variants and their mechanistic interpretation is a major challenge of modern genomics, especially for precision medicine. Transcription factor (TF) binding profiles and epigenomic landscapes in refe...
Humans Polymorphism, Single Nucleotide Female Machine Learning Models, Genetic Transcription Factors Male Gene Expression Regulation Protein Binding
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Targeting HIV/HCV Coinfection Using a Machine Learning-Based Multiple Quantitative Structure-Activity Relationships (Multiple QSAR) Method.

International journal of molecular sciences Jul 22, 2019
Human immunodeficiency virus type-1 and hepatitis C virus (HIV/HCV) coinfection occurs when a patient is simultaneously infected with both human immunodeficiency virus type-1 (HIV-1) and hepatitis C virus (HCV), which is common today in certain popul...
Quantitative Structure-Activity Relationship Databases, Pharmaceutical Polypharmacology Hepatitis C HIV-1 Molecular Conformation HIV Infections Anti-HIV Agents Antiviral Agents Protein Binding Models, Molecular Molecular Structure Bayes Theorem Humans Hepacivirus Machine Learning Algorithms Drug Discovery
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Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network.

International journal of molecular sciences Jul 12, 2019
Transcription factor binding sites (TFBSs) play an important role in gene expression regulation. Many computational methods for TFBS prediction need sufficient labeled data. However, many transcription factors (TFs) lack labeled data in cell types. W...
Neural Networks, Computer Algorithms Deep Learning ROC Curve Protein Binding Computational Biology Transcription Factors Gene Expression Regulation Organ Specificity Binding Sites
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Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites.

Proteins Jun 22, 2019
Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity or regulatory binding sites (allosteric sites), that modulate the activity of functional binding sites throu...
Algorithms Protein Binding Allosteric Site Humans Databases, Protein Evolution, Molecular Allosteric Regulation Molecular Dynamics Simulation Proteins Artificial Intelligence Protein Conformation Machine Learning Binding Sites
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Analysis of the Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach.

International journal of molecular sciences Jun 18, 2019
Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk facto...
Structure-Activity Relationship Mutation Molecular Dynamics Simulation Tumor Suppressor Protein p53 Molecular Docking Simulation Humans Protein Conformation Protein Binding Neural Networks, Computer Estrogen Receptor alpha Polymorphism, Single Nucleotide Machine Learning Protein Interaction Domains and Motifs Computational Biology
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