AIMC Topic: Amino Acid Sequence
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Deep Learning Predicts Non-Normal Transmission Distributions in High-Field Asymmetric Waveform Ion Mobility (FAIMS) Directly from Peptide Sequence.
Analytical chemistry
Jan 26, 2025
Peptide ion mobility adds an extra dimension of separation to mass spectrometry-based proteomics. The ability to accurately predict peptide ion mobility would be useful to expedite assay development and to discriminate true answers in a database sear...
GraphPhos: Predict Protein-Phosphorylation Sites Based on Graph Neural Networks.
International journal of molecular sciences
Jan 23, 2025
Phosphorylation is one of the most common protein post-translational modifications. The identification of phosphorylation sites serves as the cornerstone for protein-phosphorylation-related research. This paper proposes a protein-phosphorylation site...
IL-6-Inducing Peptide Prediction Based on 3D Structure and Graph Neural Network.
Biomolecules
Jan 10, 2025
Interleukin-6 (IL-6) is a potent glycoprotein that plays a crucial role in regulating innate and adaptive immunity, as well as metabolism. The expression and release of IL-6 are closely correlated with the severity of various diseases. IL-6-inducing ...
ConoDL: a deep learning framework for rapid generation and prediction of conotoxins.
Journal of computer-aided molecular design
Dec 26, 2024
Conotoxins, being small disulfide-rich and bioactive peptides, manifest notable pharmacological potential and find extensive applications. However, the exploration of conotoxins' vast molecular space using traditional methods is severely limited, nec...
Improved enzyme functional annotation prediction using contrastive learning with structural inference.
Communications biology
Dec 23, 2024
Recent years have witnessed the remarkable progress of deep learning within the realm of scientific disciplines, yielding a wealth of promising outcomes. A prominent challenge within this domain has been the task of predicting enzyme function, a comp...
Discovery of anticancer peptides from natural and generated sequences using deep learning.
International journal of biological macromolecules
Dec 18, 2024
Anticancer peptides (ACPs) demonstrate significant potential in clinical cancer treatment due to their ability to selectively target and kill cancer cells. In recent years, numerous artificial intelligence (AI) algorithms have been developed. However...
PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms.
Nature communications
Dec 11, 2024
Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins in cells to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards p...
Rational design of potent phosphopeptide binders to endocrine Snk PBD domain by integrating machine learning optimization, molecular dynamics simulation, binding energetics rescoring, and in vitro affinity assay.
European biophysics journal : EBJ
Nov 29, 2024
Human Snk is an evolutionarily conserved serine/threonine kinase essential for the maintenance of endocrine stability. The protein consists of a N-terminal catalytic domain and a C-terminal polo-box domain (PBD) that determines subcellular localizati...
ParaAntiProt provides paratope prediction using antibody and protein language models.
Scientific reports
Nov 25, 2024
Efficiently predicting the paratope holds immense potential for enhancing antibody design, treating cancers and other serious diseases, and advancing personalized medicine. Although traditional methods are highly accurate, they are often time-consumi...
DeepKlapred: A deep learning framework for identifying protein lysine lactylation sites via multi-view feature fusion.
International journal of biological macromolecules
Nov 19, 2024
Lysine lactylation (Kla) is a post-translational modification (PTM) that holds significant importance in the regulation of various biological processes. While traditional experimental methods are highly accurate for identifying Kla sites, they are bo...
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