AIMC Topic: Proteins

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De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution.

Chembiochem : a European journal of chemical biology Jul 12, 2023
Self-assembling polyhedral protein biomaterials have gained attention as engineering targets owing to their naturally evolved sophisticated functions, ranging from protecting macromolecules from the environment to spatially controlling biochemical re...
Artificial Intelligence Proteins Biocompatible Materials
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De novo design of protein structure and function with RFdiffusion.

Nature Jul 11, 2023
There has been considerable recent progress in designing new proteins using deep-learning methods. Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de no...
Deep Learning Protein Binding Proteins Catalytic Domain Cryoelectron Microscopy Hemagglutinin Glycoproteins, Influenza Virus
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DP-AOP: A novel SVM-based antioxidant proteins identifier.

International journal of biological macromolecules Jul 4, 2023
The identification of antioxidant proteins is a challenging yet meaningful task, as they can protect against the damage caused by some free radicals. In addition to time-consuming, laborious, and expensive experimental identification methods, efficie...
Algorithms Antioxidants Support Vector Machine Proteins
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A Highly Sensitive Model Based on Graph Neural Networks for Enzyme Key Catalytic Residue Prediction.

Journal of chemical information and modeling Jul 3, 2023
Determining the catalytic site of enzymes is a great help for understanding the relationship between protein sequence, structure, and function, which provides the basis and targets for designing, modifying, and enhancing enzyme activity. The unique l...
Neural Networks, Computer Proteins Amino Acids Amino Acid Sequence Catalytic Domain
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More than just pattern recognition: Prediction of uncommon protein structure features by AI methods.

Proceedings of the National Academy of Sciences of the United States of America Jul 3, 2023
The CASP14 experiment demonstrated the extraordinary structure modeling capabilities of artificial intelligence (AI) methods. That result has ignited a fierce debate about what these methods are actually doing. One of the criticisms has been that the...
Neural Networks, Computer Artificial Intelligence Proteins Amino Acid Sequence Protein Conformation Protein Structure, Secondary
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A deep learning solution for crystallographic structure determination.

IUCrJ Jul 1, 2023
The general de novo solution of the crystallographic phase problem is difficult and only possible under certain conditions. This paper develops an initial pathway to a deep learning neural network approach for the phase problem in protein crystallogr...
Neural Networks, Computer Deep Learning Proteins Databases, Protein Crystallography
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Finding functional motifs in protein sequences with deep learning and natural language models.

Current opinion in structural biology Jun 28, 2023
Recently, prediction of structural/functional motifs in protein sequences takes advantage of powerful machine learning based approaches. Protein encoding adopts protein language models overpassing standard procedures. Different combinations of machin...
Machine Learning Deep Learning Proteins Amino Acid Sequence
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Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15.

Proteins Jun 26, 2023
Estimating the accuracy of quaternary structural models of protein complexes and assemblies (EMA) is important for predicting quaternary structures and applying them to studying protein function and interaction. The pairwise similarity between struct...
Deep Learning Proteins Models, Molecular
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Emerging Pharmacotherapeutic Strategies to Overcome Undruggable Proteins in Cancer.

International journal of biological sciences Jun 26, 2023
Targeted therapies in cancer treatment can improve efficacy and reduce adverse effects by altering the tissue exposure of specific biomolecules. However, there are still large number of target proteins in cancer are still undruggable, owing to the f...
Humans Artificial Intelligence Neoplasms Drug Discovery Proteins Proteolysis
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A large expert-curated cryo-EM image dataset for machine learning protein particle picking.

Scientific data Jun 22, 2023
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. Howeve...
Humans Artificial Intelligence Machine Learning Animals Proteins Cryoelectron Microscopy
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