AIMC Topic: Ligands

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Ligand supplementation restores the cancer therapy efficacy of the antirheumatic drug auranofin from serum inactivation.

Nature communications Aug 9, 2025
Auranofin, an FDA-approved antirheumatic gold drug, has gained ongoing interest in clinical studies for treating advanced or recurrent tumors. However, gold ion's dynamic thiol exchange nature strongly attenuates its bioactivity due to the fast forma...
Neoplasms Antineoplastic Agents Cell Line, Tumor Female Animals Ligands Xenograft Model Antitumor Assays Antirheumatic Agents Mice Gold Sulfhydryl Compounds Humans Auranofin
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Sequence-based virtual screening using transformers.

Nature communications Jul 28, 2025
Protein-ligand interactions play central roles in myriad biological processes and are of key importance in drug design. Deep learning approaches are becoming cost-effective alternatives to high-throughput experimental methods for ligand identificatio...
Humans Drug Design Drug Evaluation, Preclinical Amino Acid Sequence Ligands Deep Learning Protein Binding Protein Kinase Inhibitors Proto-Oncogene Proteins c-abl Protein Conformation ErbB Receptors
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Augmenting MACCS Keys with Persistent Homology Fingerprints for Protein-Ligand Binding Classification.

Journal of chemical information and modeling Jul 25, 2025
Machine learning has become an essential tool in computational drug design, enabling models to uncover patterns in molecular data and predict protein-ligand interactions. This study introduces a novel approach by integrating persistence images with M...
Proteins Ligands Cheminformatics Machine Learning Drug Design Protein Binding Neural Networks, Computer
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Benchmarking 3D Structure-Based Molecule Generators.

Journal of chemical information and modeling Jul 25, 2025
To understand the benefits and drawbacks of 3D combinatorial and deep learning generators, a novel benchmark was created focusing on the recreation of important protein-ligand interactions and 3D ligand conformations. Using the BindingMOAD data set w...
Deep Learning Proteins Models, Molecular Benchmarking Ligands Molecular Conformation
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AF3Score: A Score-Only Adaptation of AlphaFold3 for Biomolecular Structure Evaluation.

Journal of chemical information and modeling Jul 16, 2025
Scoring biomolecular complexes remains central to structural modeling efforts. Recent studies suggest that AlphaFold (AF) - a revolutionary deep learning model for biomolecular structure prediction - has implicitly learned an approximate biophysical ...
Deep Learning Ligands Protein Conformation Protein Folding Protein Binding Proteins Models, Molecular
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Ligand Microenvironment-Regulated Nanozymes Enabled Machine Learning-Assisted Sensor Array for Simultaneous Identification of Phenolic Pollutants.

ACS sensors Jul 15, 2025
Phenolic pollutants pose a great threat to human health due to high toxicity, whereas existing methods are difficult to achieve the rapid recognition of multiple phenolic pollutants. In this study, we developed a novel machine learning-assisted senso...
Phenols Platinum Laccase Ligands Machine Learning Cellulose Water Pollutants, Chemical
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CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches.

Journal of computer-aided molecular design Jul 13, 2025
Identifying orthosteric binding sites and predicting small molecule affinities remains a key challenge in virtual screening. While blind docking explores the entire protein surface, its precision is hindered by the vast search space. Cavity detection...
Algorithms Molecular Docking Simulation Protein Binding Proteins Ligands Machine Learning Software Protein Conformation Binding Sites
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Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products.

Journal of computer-aided molecular design Jul 8, 2025
Mutations in isocitrate dehydrogenase 1 (IDH1) have been widely observed in various tumors, such as gliomas and acute myeloid leukemia, and therefore has become one of the current research focal points. Therefore, it is crucial to find inhibitors tha...
Binding Sites Quantitative Structure-Activity Relationship Isocitrate Dehydrogenase Humans Machine Learning Biological Products Molecular Docking Simulation Ligands Drug Discovery Enzyme Inhibitors Protein Binding
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Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces.

Journal of chemical information and modeling Jul 2, 2025
Increasing structural and biophysical evidence suggests that many drug molecules bind to the protein-membrane interface region in membrane protein structures. An important starting point for drug discovery is the determination of a ligand's binding s...
Small Molecule Libraries Models, Molecular Ligands Binding Sites Protein Binding Membrane Proteins
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EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions.

Journal of chemical information and modeling Jul 2, 2025
Accurate prediction of compound-protein interactions (CPI) remains a cornerstone challenge in computational drug discovery. While existing sequence-based approaches leverage molecular fingerprints or graph representations, they critically overlook th...
Protein Conformation Models, Molecular Ligands Drug Discovery Deep Learning Protein Binding Proteins
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