AIMC Topic: Small Molecule Libraries

Clear Filters Showing 41 to 50 of 167 articles

Binding and sensing diverse small molecules using shape-complementary pseudocycles.

Science (New York, N.Y.) Jul 18, 2024
We describe an approach for designing high-affinity small molecule-binding proteins poised for downstream sensing. We use deep learning-generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying sha...
Molecular Docking Simulation Deep Learning Methotrexate Ligands Binding Sites Protein Binding Proteins Thyroxine Nanopores Small Molecule Libraries Protein Multimerization
View on PubMed DOI

Prediction method of pharmacokinetic parameters of small molecule drugs based on GCN network model.

Journal of molecular modeling Jul 12, 2024
CONTEXT: Accurately predicting plasma protein binding rate (PPBR) and oral bioavailability (OBA) helps to better reveal the absorption and distribution of drugs in the human body and subsequent drug design. Although machine learning models have achie...
Pharmacokinetics Small Molecule Libraries Machine Learning Algorithms Protein Binding Blood Proteins Pharmaceutical Preparations Biological Availability Humans Neural Networks, Computer
View on PubMed DOI

Machine Learning Prediction of Small Molecule Accumulation in Enhanced with Descriptor Statistics.

Journal of chemical theory and computation Jul 8, 2024
Antibiotic resistance, particularly among Gram-negative bacteria, poses a significant healthcare challenge due to their ability to evade antibiotic action through various mechanisms. In this study, we explore the prediction of small molecule accumula...
Machine Learning Anti-Bacterial Agents Escherichia coli Molecular Dynamics Simulation Small Molecule Libraries
View on PubMed DOI

Predicting Collision Cross-Section Values for Small Molecules through Chemical Class-Based Multimodal Graph Attention Network.

Journal of chemical information and modeling Jul 3, 2024
Libraries of collision cross-section (CCS) values have the potential to facilitate compound identification in metabolomics. Although computational methods provide an opportunity to increase library size rapidly, accurate prediction of CCS values rema...
Machine Learning Metabolomics Small Molecule Libraries Humans
View on PubMed DOI

AlphaFold2 structures guide prospective ligand discovery.

Science (New York, N.Y.) Jun 21, 2024
AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ and serotonin 2A (5-HT2A) receptors, testing hundreds of new molecules a...
Receptors, sigma Serotonin 5-HT2 Receptor Agonists Serotonin 5-HT2 Receptor Antagonists Receptor, Serotonin, 5-HT2A Protein Conformation Cryoelectron Microscopy Small Molecule Libraries Protein Folding Drug Discovery Deep Learning Ligands Molecular Docking Simulation Drug Design Humans
View on PubMed DOI

CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks.

Journal of chemical information and modeling Jun 7, 2024
We present a novel and interpretable approach for assessing small-molecule binding using context explanation networks. Given the specific structure of a protein/ligand complex, our CENsible scoring function uses a deep convolutional neural network to...
Machine Learning Protein Binding Proteins Ligands Small Molecule Libraries Neural Networks, Computer
View on PubMed DOI

A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships.

PLoS computational biology May 20, 2024
The activities of most enzymes and drugs depend on interactions between proteins and small molecules. Accurate prediction of these interactions could greatly accelerate pharmaceutical and biotechnological research. Current machine learning models des...
Deep Learning Protein Binding Computational Biology Proteins Amino Acid Sequence Substrate Specificity Small Molecule Libraries Humans Protein Kinases Machine Learning Protein Kinase Inhibitors
View on PubMed DOI

Virtual Screening of Small Molecules Targeting BCL2 with Machine Learning, Molecular Docking, and MD Simulation.

Biomolecules May 1, 2024
This study aimed to identify potential BCL-2 small molecule inhibitors using deep neural networks (DNN) and random forest (RF), algorithms as well as molecular docking and molecular dynamics (MD) simulations to screen a library of small molecules. Th...
Small Molecule Libraries Molecular Dynamics Simulation Proto-Oncogene Proteins c-bcl-2 Machine Learning Molecular Docking Simulation Protein Binding Humans
View on PubMed DOI

Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells.

Science (New York, N.Y.) Apr 26, 2024
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advan...
Proteome Drug Discovery Ligands Protein Binding Humans Proteomics Ubiquitin-Protein Ligases Machine Learning Small Molecule Libraries
View on PubMed DOI

Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning.

Nature chemical biology Apr 17, 2024
Machine learning methods hold the promise to reduce the costs and the failure rates of conventional drug discovery pipelines. This issue is especially pressing for neurodegenerative diseases, where the development of disease-modifying drugs has been ...
Parkinson Disease Humans Structure-Activity Relationship Protein Aggregates Machine Learning alpha-Synuclein Small Molecule Libraries Drug Discovery
View on PubMed DOI
Popular Topics
Recent Journals