AIMC Topic: Drug Design

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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...
Enzyme Inhibitors Amyloid Precursor Protein Secretases Aspartic Acid Endopeptidases Drug Design Protein Binding Ligands Macrocyclic Compounds Binding Sites Humans Neural Networks, Computer Molecular Docking Simulation
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De novo generation of hit-like molecules from gene expression signatures using artificial intelligence.

Nature communications Jan 3, 2020
Finding new molecules with a desired biological activity is an extremely difficult task. In this context, artificial intelligence and generative models have been used for molecular de novo design and compound optimization. Herein, we report a generat...
Artificial Intelligence Drug Design Transcriptome Pharmaceutical Preparations 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...
Anti-Bacterial Agents Molecular Docking Simulation Drug Design Humans Machine Learning Computational Biology Neuroprotective Agents Proteins Structure-Activity Relationship Antineoplastic Agents Anti-HIV Agents Protein Binding Thermodynamics Drugs, Investigational Molecular Dynamics Simulation Ligands Binding Sites
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Rethinking drug design in the artificial intelligence era.

Nature reviews. Drug discovery Dec 4, 2019
Artificial intelligence (AI) tools are increasingly being applied in drug discovery. While some protagonists point to vast opportunities potentially offered by such tools, others remain sceptical, waiting for a clear impact to be shown in drug discov...
Artificial Intelligence Humans Drug Design Drug Discovery
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Convolutional Neural Networks for the Design and Analysis of Non-Fullerene Acceptors.

Journal of chemical information and modeling Nov 21, 2019
Convolutional neural network (CNN) is employed to construct generative and prediction models for the design and analysis of non-fullerene acceptors (NFAs) in organic solar cells. It is demonstrated that the dilated causal CNN can be trained as a good...
Electric Power Supplies Organic Chemicals Solar Energy Thermodynamics Neural Networks, Computer Drug Design
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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...
Cathepsins Protein Binding Ligands Amyloid Precursor Protein Secretases Thermodynamics Aspartic Acid Endopeptidases Molecular Docking Simulation Humans Small Molecule Libraries Binding Sites Drug Design Deep Learning
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Identification of Synthetic Activators of Cancer Cell Migration by Hybrid Deep Learning.

Chembiochem : a European journal of chemical biology Nov 14, 2019
Deep convolutional neural networks (CNNs) are a method of choice for image recognition. Herein a hybrid CNN approach is presented for molecular pattern recognition in drug discovery. Using self-organizing map images of molecular pharmacophores as inp...
Receptors, CXCR4 Humans Drug Design Deep Learning Cell Line, Tumor Cell Movement
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Artificial intelligence and big data facilitated targeted drug discovery.

Stroke and vascular neurology Nov 7, 2019
Different kinds of biological databases publicly available nowadays provide us a goldmine of multidiscipline big data. The Cancer Genome Atlas is a cancer database including detailed information of many patients with cancer. DrugBank is a database in...
Pharmacokinetics Toxicology Big Data Computer-Aided Design Structure-Activity Relationship Humans Pharmaceutical Preparations Drug Design Molecular Structure Artificial Intelligence Data Mining Drug Discovery Databases, Factual Molecular Targeted Therapy
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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...
Machine Learning Molecular Docking Simulation Drug Design Humans Databases, Protein Water Molecular Conformation Ligands Protein Binding Small Molecule Libraries Proteins
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Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.

Journal of computer-aided molecular design Oct 18, 2019
In the current "genomic era" the number of identified genes is growing exponentially. However, the biological function of a large number of the corresponding proteins is still unknown. Recognition of small molecule ligands (e.g., substrates, inhibito...
Computational Biology Proteins Models, Molecular Amino Acid Sequence Ligands Protein Conformation Software Humans Small Molecule Libraries Drug Design Sequence Homology Artificial Intelligence Protein Binding Machine Learning
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