AIMC Topic: Ligands

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Applications of machine learning in GPCR bioactive ligand discovery.

Current opinion in structural biology Apr 18, 2019
GPCRs constitute the largest druggable family having targets for 475 Food and Drug Administration (FDA) approved drugs. As GPCRs are of great interest to pharmaceutical industry, enormous efforts are being expended to find relevant and potent GPCR li...
Drug Discovery Receptors, G-Protein-Coupled Ligands Machine Learning Drug Design Humans
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Automated discovery of GPCR bioactive ligands.

Current opinion in structural biology Mar 23, 2019
While G-protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Because of the involvement of GPCRs in various signaling pathways and physiolog...
Humans Machine Learning Protein Conformation Ligands Molecular Docking Simulation Drug Discovery Drug Design Receptors, G-Protein-Coupled Molecular Dynamics Simulation
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Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning.

Journal of chemical information and modeling Mar 18, 2019
Virtual screening is a promising method for obtaining novel hit compounds in drug discovery. It aims to enrich potentially active compounds from a large chemical library for further biological experiments. However, the accuracy of current virtual scr...
Machine Learning Molecular Docking Simulation Thermodynamics Cheminformatics Drug Evaluation, Preclinical Ligands User-Computer Interface Protein Conformation Proteins
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Discovery of small molecule binders of human FSHR(TMD) with novel structural scaffolds by integrating structural bioinformatics and machine learning algorithms.

Journal of molecular graphics & modelling Mar 5, 2019
BACKGROUND: The activation of follicle stimulating hormone receptor (FSHR) by FSH and the consequent downstream signaling activities are crucial for reproductive health. The role of FSHR in tumor progression as well as osteoporosis advancement has al...
Quantitative Structure-Activity Relationship Receptors, FSH Computers, Molecular Binding Sites Models, Molecular Ligands Hydrophobic and Hydrophilic Interactions Computational Biology Cell Line Humans Drug Design Protein Binding Machine Learning
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In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening.

Journal of chemical information and modeling Mar 5, 2019
Reports of successful applications of machine learning (ML) methods in structure-based virtual screening (SBVS) are increasing. ML methods such as convolutional neural networks show promising results and often outperform traditional methods such as e...
Molecular Docking Simulation Structure-Activity Relationship Molecular Structure Databases, Factual Retrospective Studies Ligands Bias Benchmarking Machine Learning
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De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping.

Journal of chemical information and modeling Mar 5, 2019
Here we show that Generative Topographic Mapping (GTM) can be used to explore the latent space of the SMILES-based autoencoders and generate focused molecular libraries of interest. We have built a sequence-to-sequence neural network with Bidirection...
Catalytic Domain Small Molecule Libraries Receptor, Adenosine A2A Drug Evaluation, Preclinical Ligands Drug Design Deep Learning Molecular Docking Simulation
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Predicting protein-ligand binding residues with deep convolutional neural networks.

BMC bioinformatics Feb 26, 2019
BACKGROUND: Ligand-binding proteins play key roles in many biological processes. Identification of protein-ligand binding residues is important in understanding the biological functions of proteins. Existing computational methods can be roughly categ...
Databases, Protein Amino Acid Sequence Ligands Deep Learning Protein Binding Proteins Neural Networks, Computer Algorithms
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A smartphone-based system for fluorescence polarization assays.

Biosensors & bioelectronics Dec 24, 2018
This paper demonstrates the use of a smartphone-based sensor for fluorescence polarization (FP) analysis of biomolecules. The FP detection can rapidly sense ligand-analyte bindings by measuring molecule mobility, and thus, FP-based assays have been w...
Ligands Smartphone Humans Lasers Biosensing Techniques Bacterial Toxins Biomarkers Fluorescence Polarization Limit of Detection
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Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE.

Journal of chemical theory and computation Dec 24, 2018
In this work, we demonstrate how to leverage our recent iterative deep learning-all atom molecular dynamics (MD) technique "Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)" (Ribeiro, Bravo, Wang, Tiwary, J. Chem. Phys. 2018, 149...
Molecular Dynamics Simulation Ligands Deep Learning Thermodynamics Protein Binding Proteins
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Converging a Knowledge-Based Scoring Function: DrugScore.

Journal of chemical information and modeling Dec 18, 2018
We present DrugScore, a new version of the knowledge-based scoring function DrugScore, which builds upon the same formalism used to derive DrugScore but exploits a training data set of nearly 40 000 X-ray complex structures, a highly diverse and the,...
Knowledge Bases Ligands Informatics Drug Design Models, Molecular
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