AI Medical Compendium Topic:
Molecular Docking Simulation

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Introducing of an integrated artificial neural network and Chou's pseudo amino acid composition approach for computational epitope-mapping of Crimean-Congo haemorrhagic fever virus antigens.

International immunopharmacology Nov 24, 2019
This study was aimed to introduce a novel algorithm for determining linear B- and T-cell epitopes from Crimean-Congo haemorrhagic fever virus (CCHFV) antigens. To this end, 387 approved B- and T-cell epitopes, as well as 331 non-epitope peptides from...
Hemorrhagic Fever Virus, Crimean-Congo Hemorrhagic Fever, Crimean Histocompatibility Antigens Class II Epitopes, B-Lymphocyte Epitope Mapping Computational Biology Support Vector Machine Amino Acid Sequence Antigens, Viral Protein Structure, Tertiary Datasets as Topic Viral Proteins Epitopes, T-Lymphocyte Molecular Docking Simulation Peptide Library Humans Neural Networks, Computer
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MathDL: mathematical deep learning for D3R Grand Challenge 4.

Journal of computer-aided molecular design Nov 16, 2019
We present the performances of our mathematical deep learning (MathDL) models for D3R Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free energy estimation for beta secretase 1 (BACE) as well as affinity ranki...
Humans Molecular Docking Simulation Ligands Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Binding Sites Drug Design Deep Learning Protein Binding Thermodynamics Small Molecule Libraries Cathepsins
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Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S.

Journal of computer-aided molecular design Nov 15, 2019
Cathepsin S (CatS), a member of cysteine cathepsin proteases, has been well studied due to its significant role in many pathological processes, including arthritis, cancer and cardiovascular diseases. CatS inhibitors have been included in D3R-GC3 for...
Thermodynamics Cathepsins Computer-Aided Design Protein Binding Databases, Protein Humans Protein Conformation Ligands Machine Learning Binding Sites Crystallography, X-Ray Molecular Docking Simulation
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ALADDIN: Docking Approach Augmented by Machine Learning for Protein Structure Selection Yields Superior Virtual Screening Performance.

Molecular informatics Nov 8, 2019
Protein flexibility and solvation pose major challenges to docking algorithms and scoring functions. One established strategy for addressing these challenges is to use multiple protein conformations for docking (all-against-all ensemble docking). Rec...
Algorithms Proteins Machine Learning Molecular Docking Simulation Protein Conformation
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In-Silico Molecular Binding Prediction for Human Drug Targets Using Deep Neural Multi-Task Learning.

Genes Nov 7, 2019
In in-silico prediction for molecular binding of human genomes, promising results have been demonstrated by deep neural multi-task learning due to its strength in training tasks with imbalanced data and its ability to avoid over-fitting. Although the...
Molecular Docking Simulation Drug Discovery Deep Learning Protein Binding Humans Databases, Chemical Small Molecule Libraries
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Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions.

Journal of chemical information and modeling Oct 31, 2019
Structure-based drug design is critically dependent on accuracy of molecular docking scoring functions, and there is of significant interest to advance scoring functions with machine learning approaches. In this work, by judiciously expanding the tra...
Drug Design Small Molecule Libraries Water Protein Binding Humans Ligands Proteins Machine Learning Molecular Conformation Databases, Protein Molecular Docking Simulation
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A Machine Learning-Based Prediction Platform for P-Glycoprotein Modulators and Its Validation by Molecular Docking.

Cells Oct 21, 2019
P-glycoprotein (P-gp) is an important determinant of multidrug resistance (MDR) because its overexpression is associated with increased efflux of various established chemotherapy drugs in many clinically resistant and refractory tumors. This leads to...
Artificial Intelligence Machine Learning Humans Software ATP Binding Cassette Transporter, Subfamily B, Member 1 Molecular Docking Simulation Drug Discovery
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Identification of potential histone deacetylase1 (HDAC1) inhibitors using multistep virtual screening approach including SVM model, pharmacophore modeling, molecular docking and biological evaluation.

Journal of biomolecular structure & dynamics Sep 9, 2019
Histone Deacetylases (HDACs) play a significant role in the regulation of gene expression by modifying histones and non-histone substrates. Since they are key regulators in the reversible epigenetic mechanism, they are considered as promising drug ta...
Histones Histone Deacetylase Inhibitors Small Molecule Libraries Support Vector Machine Histone Deacetylases Molecular Docking Simulation Molecular Dynamics Simulation Quantitative Structure-Activity Relationship
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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...
HIV Protease HIV Protease Inhibitors Humans HIV Infections Machine Learning Protein Binding HIV-1 Molecular Docking Simulation Drug Design Drug Discovery Ligands
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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...
Thermodynamics Receptor, Insulin Protein Binding Molecular Docking Simulation Ligands Artificial Intelligence Signal Transduction Drug Discovery Receptor, IGF Type 1 Inhibitory Concentration 50 Protein Interaction Maps Algorithms Binding Sites Klotho Proteins Medicine, Chinese Traditional Antigens, CD Databases, Factual Glucuronidase
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