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Molecular Docking Simulation

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A Review on Applications of Computational Methods in Drug Screening and Design.

Molecules (Basel, Switzerland) Mar 18, 2020
Drug development is one of the most significant processes in the pharmaceutical industry. Various computational methods have dramatically reduced the time and cost of drug discovery. In this review, we firstly discussed roles of multiscale biomolecul...
Molecular Dynamics Simulation Molecular Docking Simulation Drug Design Drug Discovery Machine Learning
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Energy-based graph convolutional networks for scoring protein docking models.

Proteins Mar 16, 2020
Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative for su...
Humans Software Research Design Proteins Benchmarking Amino Acid Sequence Ligands Peptides Molecular Docking Simulation Deep Learning Protein Binding Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Mapping Binding Sites Protein Multimerization Thermodynamics Protein Interaction Domains and Motifs Computer Graphics Structural Homology, Protein
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Combining Docking Pose Rank and Structure with Deep Learning Improves Protein-Ligand Binding Mode Prediction over a Baseline Docking Approach.

Journal of chemical information and modeling Mar 3, 2020
We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by a standard...
Molecular Docking Simulation Deep Learning Protein Binding Proteins Ligands
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Discovery of Small-Molecule Activators for Glucose-6-Phosphate Dehydrogenase (G6PD) Using Machine Learning Approaches.

International journal of molecular sciences Feb 23, 2020
Glucose-6-Phosphate Dehydrogenase (G6PD) is a ubiquitous cytoplasmic enzyme converting glucose-6-phosphate into 6-phosphogluconate in the pentose phosphate pathway (PPP). The G6PD deficiency renders the inability to regenerate glutathione due to lack...
Drug Discovery Oxidative Stress Oxidation-Reduction Glucosephosphate Dehydrogenase Deficiency Machine Learning Protein Interaction Domains and Motifs Animals Molecular Docking Simulation Drug Evaluation, Preclinical Glucosephosphate Dehydrogenase Humans NADP Pentose Phosphate Pathway Catalytic Domain Glutathione X-Ray Diffraction
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Prediction of Contact Residues in Anti-HIV Neutralizing Antibody by Deep Learning.

Japanese journal of infectious diseases Jan 31, 2020
The monoclonal antibody 1C10 targets the V3 loop of HIV-1 and neutralizes a broad range of clade B viruses. However, the mode of interaction between 1C10 and the V3 loop remains unclear because crystallization of 1C10 and the V3 peptide was unsuccess...
HIV Antibodies HIV Envelope Protein gp120 Binding Sites, Antibody Humans Molecular Docking Simulation Peptide Fragments Deep Learning Antibodies, Neutralizing Antibodies, Monoclonal Amino Acid Sequence Amino Acid Substitution
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Design of (quinolin-4-ylthio)carboxylic acids as new Escherichia coli DNA gyrase B inhibitors: machine learning studies, molecular docking, synthesis and biological testing.

Computational biology and chemistry Jan 24, 2020
Spread of multidrug-resistant Escherichia coli clinical isolates is a main problem in the treatment of infectious diseases. Therefore, the modern scientific approaches in decision this problem require not only a prevention strategy, but also the deve...
Machine Learning Anti-Bacterial Agents Quantitative Structure-Activity Relationship Computational Biology Molecular Docking Simulation Escherichia coli Quinolines Molecular Structure Drug Design DNA Gyrase Microbial Sensitivity Tests Topoisomerase II Inhibitors
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Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4.

Journal of computer-aided molecular design Jan 8, 2020
Drug Design Data Resource (D3R) Grand Challenge 4 (GC4) offered a unique opportunity for designing and testing novel methodology for accurate docking and affinity prediction of ligands in an open and blinded manner. We participated in the beta-secret...
Protein Binding Ligands Enzyme Inhibitors Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Macrocyclic Compounds Binding Sites Humans Neural Networks, Computer Molecular Docking Simulation Drug Design
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A mitochondria-targeting nitroreductase fluorescent probe with large Stokes shift and long-wavelength emission for imaging hypoxic status in tumor cells.

Analytica chimica acta Dec 24, 2019
Development of a mitochondria-targeting fluorescent probe with large Stokes shift and long-wavelength emission was benefit for accurate detection of hypoxic status, which was known as a major factor of the tumor physiology and influence important pat...
Microscopy, Fluorescence Protein Binding Humans Mitochondria Nitroreductases Limit of Detection Molecular Docking Simulation Benzothiazoles Pyridinium Compounds Spectrometry, Fluorescence Cell Line, Tumor Cell Hypoxia Quinolinium Compounds Fluorescent Dyes
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Latest trends in structure based drug design with protein targets.

Advances in protein chemistry and structural biology Dec 18, 2019
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to d...
Binding Sites Thermodynamics Drugs, Investigational Molecular Docking Simulation Proteins Drug Design Structure-Activity Relationship Antineoplastic Agents Molecular Dynamics Simulation Anti-HIV Agents Ligands Humans Protein Binding Machine Learning Computational Biology Anti-Bacterial Agents Neuroprotective Agents
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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...
Peptides Molecular Docking Simulation Antineoplastic Agents Blood Glucose Blood Pressure Humans Neural Networks, Computer Algorithms Neoplasms
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