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Molecular Docking Simulation

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Machine-Learning-Assisted Approach for Discovering Novel Inhibitors Targeting Bromodomain-Containing Protein 4.

Journal of chemical information and modeling Jul 10, 2017
Bromodomain-containing protein 4 (BRD4) is implicated in the pathogenesis of a number of different cancers, inflammatory diseases and heart failure. Much effort has been dedicated toward discovering novel scaffold BRD4 inhibitors (BRD4is) with differ...
Humans Machine Learning Molecular Docking Simulation Drug Discovery Drug Evaluation, Preclinical Molecular Targeted Therapy Protein Conformation Cell Cycle Proteins Nuclear Proteins Transcription Factors Cell Line Structure-Activity Relationship
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Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Protein Multimerization Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Animals Proteins Protein Conformation, beta-Strand Humans Molecular Docking Simulation Binding Sites Protein Binding Machine Learning Thermodynamics Computational Biology Protein Interaction Mapping
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Protein-Protein Interaction Interface Residue Pair Prediction Based on Deep Learning Architecture.

IEEE/ACM transactions on computational biology and bioinformatics May 19, 2017
MOTIVATION: Proteins usually fulfill their biological functions by interacting with other proteins. Although some methods have been developed to predict the binding sites of a monomer protein, these are not sufficient for prediction of the interactio...
Molecular Docking Simulation Deep Learning Protein Binding Protein Conformation Binding Sites Computational Biology Proteins Surface Properties
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InterPred: A pipeline to identify and model protein-protein interactions.

Proteins Mar 21, 2017
Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the numb...
Computational Biology Support Vector Machine Proteins Internet Software Molecular Docking Simulation Protein Interaction Domains and Motifs Benchmarking Amino Acid Sequence Protein Interaction Mapping Sequence Analysis, Protein
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Predicting DPP-IV inhibitors with machine learning approaches.

Journal of computer-aided molecular design Feb 2, 2017
Dipeptidyl peptidase IV (DPP-IV) is a promising Type 2 diabetes mellitus (T2DM) drug target. DPP-IV inhibitors prolong the action of glucagon-like peptide-1 (GLP-1) and gastric inhibitory peptide (GIP), improve glucose homeostasis without weight gain...
Small Molecule Libraries Dipeptidyl-Peptidase IV Inhibitors Humans Machine Learning Molecular Docking Simulation Computer-Aided Design Drug Design Diabetes Mellitus, Type 2 Bayes Theorem Dipeptidyl Peptidase 4
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Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.

PloS one Jan 24, 2017
Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scorin...
Software Algorithms Computer Simulation Protein Interaction Mapping Molecular Docking Simulation Knowledge Bases Protein Binding Linear Models Models, Molecular Protein Conformation Models, Chemical Monte Carlo Method
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Machine learning and docking models for Mycobacterium tuberculosis topoisomerase I.

Tuberculosis (Edinburgh, Scotland) Jan 20, 2017
There is a shortage of compounds that are directed towards new targets apart from those targeted by the FDA approved drugs used against Mycobacterium tuberculosis. Topoisomerase I (Mttopo I) is an essential mycobacterial enzyme and a promising target...
Molecular Targeted Therapy Protein Conformation Mycobacterium smegmatis DNA Topoisomerases, Type I Topoisomerase I Inhibitors Humans Machine Learning Molecular Docking Simulation Bayes Theorem Computer-Aided Design Antitubercular Agents Tuberculosis Drug Design Mycobacterium tuberculosis Dose-Response Relationship, Drug Structure-Activity Relationship
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A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison.

Proteins Jan 20, 2017
Reliable identification of near-native poses of docked protein-protein complexes is still an unsolved problem. The intrinsic heterogeneity of protein-protein interactions is challenging for traditional biophysical or knowledge based potentials and th...
Binding Sites Thermodynamics Protein Interaction Mapping Structural Homology, Protein Proteins Benchmarking Protein Conformation Machine Learning Software Research Design Molecular Docking Simulation Protein Binding Computational Biology Cluster Analysis
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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...
Benzoic Acid Pyrazoles Drug Resistance, Multiple, Bacterial Gram-Negative Bacteria Binding Sites Anti-Infective Agents Gram-Positive Bacteria Structure-Activity Relationship Molecular Docking Simulation Catalytic Domain Microbial Sensitivity Tests Acinetobacter baumannii
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Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility.

Proteins Dec 5, 2016
Predicting protein conformational changes from unbound structures or even homology models to bound structures remains a critical challenge for protein docking. Here we present a study directly addressing the challenge by reducing the dimensionality a...
Proteins Benchmarking Protein Conformation Dimensional Measurement Accuracy Machine Learning Molecular Docking Simulation Binding Sites Software Thermodynamics Research Design Protein Binding Protein Multimerization Computational Biology Structural Homology, Protein Models, Statistical
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