AIMC Topic: Molecular Structure

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DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges.

Briefings in bioinformatics May 20, 2021
Atomic charges play a very important role in drug-target recognition. However, computation of atomic charges with high-level quantum mechanics (QM) calculations is very time-consuming. A number of machine learning (ML)-based atomic charge prediction ...
Molecular Structure Quantum Theory Machine Learning Drug Design Neural Networks, Computer
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Beware of the generic machine learning-based scoring functions in structure-based virtual screening.

Briefings in bioinformatics May 20, 2021
Machine learning-based scoring functions (MLSFs) have attracted extensive attention recently and are expected to be potential rescoring tools for structure-based virtual screening (SBVS). However, a major concern nowadays is whether MLSFs trained for...
Machine Learning Protein Binding Molecular Structure Datasets as Topic Drug Discovery User-Computer Interface Molecular Docking Simulation
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A graph-convolutional neural network for addressing small-scale reaction prediction.

Chemical communications (Cambridge, England) Apr 27, 2021
We describe a graph-convolutional neural network (GCN) model, the reaction prediction capabilities of which are as potent as those of the transformer model based on sufficient data, and we adopt the Baeyer-Villiger oxidation reaction to explore their...
Neural Networks, Computer Molecular Structure Humans Databases, Factual Oxidation-Reduction
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Application and assessment of deep learning for the generation of potential NMDA receptor antagonists.

Physical chemistry chemical physics : PCCP Jan 21, 2021
Uncompetitive antagonists of the N-methyl d-aspartate receptor (NMDAR) have demonstrated therapeutic benefit in the treatment of neurological diseases such as Parkinson's and Alzheimer's, but some also cause dissociative effects that have led to the ...
Receptors, N-Methyl-D-Aspartate Binding Sites Xenopus laevis Small Molecule Libraries Mice Molecular Structure Drug Design Animals Ligands Deep Learning
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DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes.

Proceedings of the National Academy of Sciences of the United States of America Jan 12, 2021
Information about macromolecular structure of protein complexes and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully aut...
Molecular Structure SARS-CoV-2 Cryoelectron Microscopy Models, Structural Deep Learning Viral Proteins
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canSAR: update to the cancer translational research and drug discovery knowledgebase.

Nucleic acids research Jan 8, 2021
canSAR (http://cansar.icr.ac.uk) is the largest, public, freely available, integrative translational research and drug discovery knowledgebase for oncology. canSAR integrates vast multidisciplinary data from across genomic, protein, pharmacological, ...
Antineoplastic Agents User-Computer Interface Genomics Neoplasms Drug Discovery Databases, Genetic Molecular Structure Internet Computational Biology Proteomics Humans Medical Oncology Translational Research, Biomedical Data Mining Knowledge Bases
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Parsing Sage and Rosemary in Time: The Machine Learning Race to Crack Olfactory Perception.

Chemical senses Jan 1, 2021
Color and pitch perception are largely understandable from characteristics of physical stimuli: the wavelengths of light and sound waves, respectively. By contrast, understanding olfactory percepts from odorous stimuli (volatile molecules) is much mo...
Olfactory Perception Molecular Structure Odorants Volatile Organic Compounds Machine Learning Humans Time Factors
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A System-Wide Understanding of the Human Olfactory Percept Chemical Space.

Chemical senses Jan 1, 2021
The fundamental units of olfactory perception are discrete 3D structures of volatile chemicals that each interact with specific subsets of a very large family of hundreds of odorant receptor proteins, in turn activating complex neural circuitry and p...
Software Machine Learning Molecular Structure Humans Odorants Smell Olfactory Perception Volatile Organic Compounds
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Identification of novel CDK2 inhibitors by a multistage virtual screening method based on SVM, pharmacophore and docking model.

Journal of enzyme inhibition and medicinal chemistry Dec 1, 2020
Cyclin-dependent kinase 2 (CDK2) is the family of Ser/Thr protein kinases that has emerged as a highly selective with low toxic cancer therapy target. A multistage virtual screening method combined by SVM, protein-ligand interaction fingerprints (PLI...
Structure-Activity Relationship Protein Kinase Inhibitors Drug Evaluation, Preclinical A549 Cells Cyclin-Dependent Kinase 2 HCT116 Cells Cell Proliferation Dose-Response Relationship, Drug Humans Molecular Structure Support Vector Machine Molecular Docking Simulation Drug Screening Assays, Antitumor Antineoplastic Agents
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Classification of biomass reactions and predictions of reaction energies through machine learning.

The Journal of chemical physics Jul 28, 2020
Elementary steps and intermediate species of linearly structured biomass compounds are studied. Specifically, possible intermediates and elementary reactions of 15 key biomass compounds and 33 small molecules are obtained from a recursive bond-breaki...
Biomass Machine Learning Molecular Structure Algorithms Discriminant Analysis
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