AIMC Topic: Amino Acid Sequence

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Ai-driven de novo design of customizable membrane permeable cyclic peptides.

Journal of computer-aided molecular design Aug 9, 2025
Cyclic peptides, prized for their remarkable bioactivity and stability, hold great promise across various fields. Yet, designing membrane-penetrating bioactive cyclic peptides via traditional methods is complex and resource-intensive. To address this...
Artificial Intelligence Drug Design Peptides, Cyclic Cell Membrane Permeability Cell-Penetrating Peptides Molecular Dynamics Simulation Amino Acid Sequence
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Bag-of-words is competitive with sum-of-embeddings language-inspired representations on protein inference.

PloS one Aug 6, 2025
Inferring protein function is a fundamental and long-standing problem in biology. Laboratory experiments in this field are often expensive, and therefore large-scale computational protein inference from readily available amino acid sequences is neede...
Algorithms Computational Biology Databases, Protein Natural Language Processing Proteins Amino Acid Sequence Sequence Analysis, Protein
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PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context.

Nature communications Aug 5, 2025
Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenici...
Protein Conformation Proteins Mutation, Missense Amino Acid Sequence Neural Networks, Computer Deep Learning Computational Biology Humans
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Multimodal deep learning for allergenic proteins prediction.

BMC biology Jul 31, 2025
BACKGROUND: Accurate prediction of allergens is essential for identifying the sources of allergic reactions and preventing future exposure to harmful triggers; however, the limited performance of current prediction tools hinders their practical appli...
Epitopes Amino Acid Sequence Humans Deep Learning Allergens
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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...
Ligands Protein Conformation Protein Kinase Inhibitors Proto-Oncogene Proteins c-abl ErbB Receptors Drug Evaluation, Preclinical Amino Acid Sequence Deep Learning Protein Binding Humans Drug Design
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BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information.

BMC bioinformatics Jul 21, 2025
Bioactive peptides are beneficial or have physiological effects on the life activities of biological organisms. The functions of bioactive peptides are diverse, usually with one or more, so accurately detecting the multiple functions of multi-functio...
Peptides Deep Learning Computational Biology Amino Acid Sequence
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Cysteine pattern barcoding-based dataset filtration enhances the machine learning-assisted interpretation of Conus venom peptide therapeutics.

PloS one Jul 11, 2025
Crude cone snail venom is a rich source of bioactive compounds with significant therapeutic potential. In this study, we conducted a comprehensive analysis of 5,985 cone snail peptides across 82 Conus species to identify unique cysteine (Cys) pattern...
Machine Learning Animals Amino Acid Sequence Cysteine Peptides Mollusk Venoms Conotoxins Conus Snail
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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...
Amino Acid Sequence Protein Conformation Proteins Models, Molecular Neural Networks, Computer Humans Peptides Deep Learning
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Machine learning driven dashboard for chronic myeloid leukemia prediction using protein sequences.

PloS one Jun 18, 2025
The prevalence of Leukaemia, a malignant blood cancer that originates from hematopoietic progenitor cells, is increasing in Southeast Asia, with a worrisome fatality rate of 54%. Predicting outcomes in the early stages is vital for improving the chan...
Proto-Oncogene Proteins c-bcl-2 Leukemia, Myelogenous, Chronic, BCR-ABL Positive Support Vector Machine Amino Acid Sequence Humans Machine Learning
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AI, docking, and molecular dynamics to track the binding of structural peptides to different keratin models.

International journal of biological macromolecules May 30, 2025
The present work shows a computational approach to assess the interactions of different nature-inspired peptides with hair keratin models. An updated keratin model was validated, and comparisons with previous models were traced, thereby highlighting ...
Molecular Dynamics Simulation Amino Acid Sequence Molecular Docking Simulation Protein Binding Artificial Intelligence Peptides Keratins
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