AIMC Topic: Molecular Docking Simulation

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Prediction of the Health Effects of Food Peptides and Elucidation of the Mode-of-action Using Multi-task Graph Convolutional Neural Network.

Molecular informatics Nov 28, 2019
Food proteins work not only as nutrients but also modulators for the physiological functions of the human body. The physiological functions of food proteins are basically regulated by peptides encrypted in food protein sequences (food peptides). In t...
Molecular Docking Simulation Antineoplastic Agents Blood Glucose Blood Pressure Humans Algorithms Neural Networks, Computer Neoplasms Peptides
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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 Viral Proteins Antigens, Viral Protein Structure, Tertiary Histocompatibility Antigens Class II Epitopes, B-Lymphocyte Epitope Mapping Neural Networks, Computer Epitopes, T-Lymphocyte Humans Support Vector Machine Amino Acid Sequence Molecular Docking Simulation Datasets as Topic Peptide Library Computational Biology
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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...
Molecular Docking Simulation Drug Design Deep Learning Humans Aspartic Acid Endopeptidases Binding Sites Thermodynamics Small Molecule Libraries Protein Binding Ligands Amyloid Precursor Protein Secretases 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...
Cathepsins Databases, Protein Molecular Docking Simulation Ligands Computer-Aided Design Humans Crystallography, X-Ray Protein Conformation Protein Binding Machine Learning Binding Sites Thermodynamics
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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 Molecular Docking Simulation Proteins Protein Conformation Machine Learning
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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...
Drug Discovery Deep Learning Protein Binding Humans Molecular Docking Simulation 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...
Water Protein Binding Proteins Databases, Protein Small Molecule Libraries Machine Learning Ligands Humans Molecular Docking Simulation Molecular Conformation Drug Design
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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...
Machine Learning Software Molecular Docking Simulation Humans Artificial Intelligence Drug Discovery ATP Binding Cassette Transporter, Subfamily B, Member 1
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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 Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Molecular Docking Simulation Histone Deacetylases
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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...
Protein Binding HIV-1 Ligands Drug Design Humans HIV Protease Drug Discovery Machine Learning HIV Protease Inhibitors HIV Infections Molecular Docking Simulation
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