AIMC Topic: Models, Molecular

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Integrating Protein Language Models and Geometric Deep Learning for Peptide Toxicity Prediction.

Journal of chemical information and modeling Jul 8, 2025
Peptide toxicity prediction is a critical task in biomedical research, influencing drug safety and therapeutic development. Traditional methods, relying on sequence similarity or handcrafted features, struggle to capture the complex relationship betw...
Protein Conformation Amino Acid Sequence Peptides Deep Learning Proteins Models, Molecular Humans Neural Networks, Computer
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Mapping the Conformational Heterogeneity Intrinsic to the Protein Native Ensemble.

Biochemistry Jul 4, 2025
In the AlphaFold era, there is a significant momentum in predicting protein structures, functionality, and mutational hotspots from deep learning approaches. In this review, we highlight how structural information is only a starting point in understa...
Protein Folding Humans Proteins Models, Molecular Protein Conformation
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MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures.

Nature communications Jul 4, 2025
At sufficiently high resolution, x-ray crystallography and cryogenic electron microscopy are capable of resolving small spherical map features corresponding to either water or ions. Correct classification of these sites provides crucial insight for u...
Deep Learning Water Proteins Crystallography, X-Ray Models, Molecular Cryoelectron Microscopy Ions
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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...
Membrane Proteins Ligands Protein Binding Small Molecule Libraries Models, Molecular Binding Sites
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Predicting RNA Structure Utilizing Attention from Pretrained Language Models.

Journal of chemical information and modeling Jul 2, 2025
RNA possesses functional significance that extends beyond the transport of genetic information. The functional roles of noncoding RNA can be mediated through their tertiary and secondary structure, and thus, predicting RNA structure holds great promi...
Natural Language Processing Models, Molecular Nucleic Acid Conformation Computational Biology RNA
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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 Deep Learning Protein Binding Models, Molecular Drug Discovery Proteins Ligands
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Robust Lightweight Graph Neural Network Framework for Accelerating Crystal Structure Prediction.

Journal of chemical information and modeling Jun 30, 2025
This work presents a crystal structure prediction framework that employs a structural search using a derivative-free optimization method, with a supervised Graph Neural Network (GNN) model as the energy evaluator. We address the limitations of existi...
Neural Networks, Computer Crystallography, X-Ray Graph Neural Networks Models, Molecular Bayes Theorem
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Scaffold Hopping with Generative Reinforcement Learning.

Journal of chemical information and modeling Jun 26, 2025
Scaffold hopping-the design of novel scaffolds for existing lead candidates-is a multifaceted and nontrivial task, for medicinal chemists and computational approaches alike. Generative reinforcement learning can iteratively optimize desirable propert...
Drug Design Models, Molecular Machine Learning
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Sequence and Structure-based Prediction of Allosteric Sites.

Journal of molecular biology Jun 24, 2025
Allosteric regulation in proteins is a critical aspect of cellular function, influencing various biological processes through conformational or dynamic changes induced by effector molecules. Allosteric drugs possess significant therapeutic value due ...
Proteins Models, Molecular Humans Drug Design Computational Biology Amino Acid Sequence Allosteric Site Protein Conformation Allosteric Regulation
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HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes.

Journal of chemical information and modeling Jun 17, 2025
HADDOCK is a widely used resource for integrative modeling of a variety of biomolecular complexes that is able to incorporate experimental knowledge into physics-based calculations during complex prediction, refinement, scoring and analysis. Here we ...
Software Proteins Models, Molecular
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