AIMC Topic: Amino Acid Sequence

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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...
Amino Acid Sequence Proto-Oncogene Proteins c-bcl-2 Leukemia, Myelogenous, Chronic, BCR-ABL Positive Machine Learning Support Vector Machine Humans
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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 Docking Simulation Protein Binding Molecular Dynamics Simulation Artificial Intelligence Peptides Amino Acid Sequence Keratins
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Cyclic peptide structure prediction and design using AlphaFold2.

Nature communications May 21, 2025
Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here...
Crystallography, X-Ray Protein Conformation Proto-Oncogene Proteins c-mdm2 Amino Acid Sequence Peptides, Cyclic Kelch-Like ECH-Associated Protein 1 Humans Drug Design Deep Learning Computational Biology Models, Molecular
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Machine learning models for predicting configuration of modified knuckle epitope peptides of BMP-2 protein using mesoscale simulation data.

Physical chemistry chemical physics : PCCP Apr 30, 2025
The high doses of bone morphogenetic proteins (BMPs) cause undesired side effects in skeletal tissue regeneration. An alternative approach is to use the bioactive knuckle epitope domain of BMP-2 (BMP2-KEP) with an open-arm structure as part of the pr...
Models, Molecular Humans Epitopes Machine Learning Amino Acid Sequence Quantitative Structure-Activity Relationship Peptides Bone Morphogenetic Protein 2
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Dynamics and Machine Learning Reveal the Link between Tripeptide Sequences and Evaporation-Driven Material Properties.

Nano letters Apr 27, 2025
Previous research showed that a peptide composed of three tyrosines (YYY) can turn into organic glass and cause strong adhesion between substrates via evaporation. However, the mechanisms of these processes remain unclear, and the exploration of appl...
Hydrogen Bonding Surface Properties Oligopeptides Machine Learning Peptides Amino Acid Sequence Water Dimethylpolysiloxanes Molecular Dynamics Simulation Hydrophobic and Hydrophilic Interactions
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Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.

Cell Apr 23, 2025
In humans, selective and promiscuous interactions between 46 secreted chemokine ligands and 23 cell surface chemokine receptors of the G-protein-coupled receptor (GPCR) family form a complex network to coordinate cell migration. While chemokines and ...
Ligands Humans Chemokines Receptors, G-Protein-Coupled Protein Binding Receptors, Chemokine Models, Molecular Amino Acid Sequence
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Neural network conditioned to produce thermophilic protein sequences can increase thermal stability.

Scientific reports Apr 23, 2025
This work presents Neural Optimization for Melting-temperature Enabled by Leveraging Translation (NOMELT), a novel approach for designing and ranking high-temperature stable proteins using neural machine translation. The model, trained on over 4 mill...
Animals Transcription Factors Amino Acid Sequence Protein Stability Drosophila Proteins Drosophila melanogaster Neural Networks, Computer Homeodomain Proteins Temperature
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Optimizing lipocalin sequence classification with ensemble deep learning models.

PloS one Apr 16, 2025
Deep learning (DL) has become a powerful tool for the recognition and classification of biological sequences. However, conventional single-architecture models often struggle with suboptimal predictive performance and high computational costs. To addr...
Lipocalins Deep Learning Humans Computational Biology Neural Networks, Computer Amino Acid Sequence
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Predicting protein-protein interaction with interpretable bilinear attention network.

Computer methods and programs in biomedicine Mar 30, 2025
BACKGROUND AND OBJECTIVE: Protein-protein interactions (PPIs) play the key roles in myriad biological processes, helping to understand the protein function and disease pathology. Identification of PPIs and their interaction types through wet experime...
Sequence Analysis, Protein Deep Learning Protein Binding Protein Conformation Protein Interaction Mapping Computational Biology Humans Proteins Neural Networks, Computer Databases, Protein Algorithms Amino Acid Sequence
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Atomic context-conditioned protein sequence design using LigandMPNN.

Nature methods Mar 28, 2025
Protein sequence design in the context of small molecules, nucleotides and metals is critical to enzyme and small-molecule binder and sensor design, but current state-of-the-art deep-learning-based sequence design methods are unable to model nonprote...
Crystallography, X-Ray Deep Learning Protein Conformation Protein Binding Amino Acid Sequence Proteins Ligands Models, Molecular
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