AIMC Topic: Models, Molecular

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Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning.

Journal of chemical information and modeling Nov 26, 2025
Protein structure database search has become increasingly challenging due to the growing number of experimental and computational structures. We introduce mTM-align2, a novel two-step approach for rapid and accurate protein structure database search....
Machine Learning Time Factors Models, Molecular Protein Conformation Protein Folding Proteins Databases, Protein
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High-accuracy protein complex structure modeling based on sequence-derived structure complementarity.

Nature communications Nov 19, 2025
In living organisms, proteins perform key functions required for life activities by interacting to form complexes. Determining the protein complex structure is crucial for understanding and mastering biological functions. Although AlphaFold2 makes a ...
Sequence Alignment Models, Molecular Protein Conformation Deep Learning Proteins Computational Biology Databases, Protein
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Modeling protein-small molecule conformational ensembles with PLACER.

Proceedings of the National Academy of Sciences of the United States of America Nov 4, 2025
Modeling the conformational heterogeneity of protein-small molecule interactions is important for understanding natural systems and evaluating designed systems but remains an outstanding challenge. We reasoned that while residue-level descriptions of...
Neural Networks, Computer Molecular Docking Simulation Small Molecule Libraries Models, Molecular Proteins Ligands Databases, Protein Protein Conformation
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From sequence to scaffold: Computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks.

Proceedings of the National Academy of Sciences of the United States of America Nov 3, 2025
Self-assembling protein nanoparticles are being increasingly utilized in the design of next-generation vaccines due to their ability to induce antibody responses of superior magnitude, breadth, and durability. Computational protein design offers a ro...
Models, Molecular Vaccines Influenza Vaccines Computational Biology Nanoparticles Nanovaccines Cryoelectron Microscopy Hemagglutinin Glycoproteins, Influenza Virus Animals Mice Machine Learning
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Geometry-Driven Attention Model with 3D Molecular Features for Multi-Property Prediction of OLED Materials.

Journal of chemical information and modeling Oct 31, 2025
As Organic Light-Emitting Diode (OLED) technology advances in applications such as high-end displays, medical devices, and VR/AR systems, the development of high-performance materials that improve energy efficiency and support environmental sustainab...
Deep Learning Models, Molecular
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In silico Techniques for the Investigation of Bioactive Compounds in Quinoa (Chenopodium quinoa Willd.): Recent Advances in Molecular Modeling and Identification of Therapeutic Targets.

Plant foods for human nutrition (Dordrecht, Netherlands) Oct 29, 2025
Quinoa (Chenopodium quinoa Willd.) is a valuable source of bioactive compounds with therapeutic potential, including peptides, saponins, and polyphenols. In recent years, in silico tools have emerged as key strategies for predicting, characterizing, ...
Molecular Dynamics Simulation Saponins Chenopodium quinoa Phytochemicals Models, Molecular Computer Simulation Peptides Polyphenols Flavonoids Molecular Docking Simulation Humans
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3d electron cloud descriptors for enhanced QSAR modeling of anti-colorectal cancer compounds.

Journal of computer-aided molecular design Oct 24, 2025
To address limitations of conventional Quantitative Structure-Activity Relationship (QSAR) descriptors in capturing molecular electronic and spatial complexity, we developed a high-dimensional framework using three-dimensional electron density featur...
Models, Molecular Electrons Quantitative Structure-Activity Relationship Antineoplastic Agents Density Functional Theory Humans Machine Learning Colorectal Neoplasms
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Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors.

Journal of computer-aided molecular design Oct 24, 2025
The interaction between staphylococcal protein A (SpA) and human immunoglobulin G (IgG) is pivotal in treating diseases such as cancer, inflammation, infections, and autoimmune disorders. However, acquiring natural SpA variants is labor-intensive, tr...
Humans Immunoglobulin G Protein Binding Models, Molecular Deep Learning Protein Engineering Staphylococcal Protein A Mutation Binding Sites
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Predicting protein-protein interactions in the human proteome.

Science (New York, N.Y.) Oct 23, 2025
Protein-protein interactions (PPIs) are essential for biological function. Coevolutionary analysis and deep-learning (DL)-based protein structure prediction have enabled comprehensive PPI identification in bacteria and yeast, but these approaches hav...
Protein Conformation Protein Interaction Mapping Protein Interaction Maps Humans Deep Learning Proteome Sequence Alignment Models, Molecular
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AQuaRef: machine learning accelerated quantum refinement of protein structures.

Nature communications Oct 17, 2025
Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical enti...
Quantum Theory Proteins Humans Crystallography, X-Ray Hydrogen Bonding Machine Learning Models, Molecular Protein Conformation Cryoelectron Microscopy
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