AIMC Topic: Ligands

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Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease.

Journal of chemical theory and computation Jan 16, 2020
Over the past several decades, atomistic simulations of biomolecules, whether carried out using molecular dynamics or Monte Carlo techniques, have provided detailed insights into their function. Comparing the results of such simulations for a few clo...
Machine Learning Protein Binding Mutation Molecular Dynamics Simulation Humans HIV Protease Inhibitors Hydrogen Bonding Static Electricity Monte Carlo Method HIV-1 Ligands Drug Resistance, Viral HIV Protease
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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...
Macrocyclic Compounds Binding Sites Molecular Docking Simulation Drug Design Protein Binding Ligands Enzyme Inhibitors Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Humans Neural Networks, Computer
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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...
Drugs, Investigational Molecular Dynamics Simulation Ligands Binding Sites Thermodynamics Neuroprotective Agents Proteins Structure-Activity Relationship Machine Learning Anti-Bacterial Agents Molecular Docking Simulation Drug Design Antineoplastic Agents Humans Anti-HIV Agents Protein Binding Computational Biology
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Comprehensive Exploration of Target-specific Ligands Using a Graph Convolution Neural Network.

Molecular informatics Dec 9, 2019
Machine learning approaches are widely used to evaluate ligand activities of chemical compounds toward potential target proteins. Especially, exploration of highly selective ligands is important for the development of new drugs with higher safety. On...
Humans Neural Networks, Computer Aspartic Acid Endopeptidases Cathepsin D Algorithms Ligands Amyloid Precursor Protein Secretases
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers.

Progress in molecular biology and translational science Dec 6, 2019
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfam...
Receptors, G-Protein-Coupled Mutation Molecular Dynamics Simulation Ligands Protein Binding Computational Biology Support Vector Machine Protein Multimerization Allosteric Site Fluorescence Resonance Energy Transfer Crystallography, X-Ray Protein Interaction Mapping Protein Structure, Secondary Humans Neural Networks, Computer Machine Learning Software Algorithms Animals
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Development of New Methods Needs Proper Evaluation-Benchmarking Sets for Machine Learning Experiments for Class A GPCRs.

Journal of chemical information and modeling Nov 22, 2019
New computational approaches for virtual screening applications are constantly being developed. However, before a particular tool is used to search for new active compounds, its effectiveness in the type of task must be examined. In this study, we co...
Benchmarking Drug Evaluation, Preclinical Machine Learning Ligands User-Computer Interface Receptors, G-Protein-Coupled
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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...
Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Binding Sites Thermodynamics Deep Learning Protein Binding Ligands Humans Small Molecule Libraries Molecular Docking Simulation Cathepsins Drug Design
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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...
Binding Sites Thermodynamics Cathepsins Ligands Crystallography, X-Ray Molecular Docking Simulation Protein Conformation Computer-Aided Design Protein Binding Humans Databases, Protein Machine Learning
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Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions.

Journal of computer-aided molecular design Nov 14, 2019
The computational prediction of ligand-biopolymer affinities is a crucial endeavor in modern drug discovery and one that still poses major challenges. The choice of the appropriate computational method often reveals itself as a trade-off between accu...
Machine Learning Algorithms Drug Discovery Protein Binding Proteins Databases, Protein Ligands Humans
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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...
Databases, Protein Drug Design Humans Small Molecule Libraries Ligands Machine Learning Water Molecular Conformation Molecular Docking Simulation Protein Binding Proteins
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