AIMC Topic: Peptides

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AI-Assisted Processing Pipeline to Boost Protein Isoform Detection.

Methods in molecular biology (Clifton, N.J.)
Proteomics, the study of proteins within biological systems, has seen remarkable advancements in recent years, with protein isoform detection emerging as one of the next major frontiers. One of the primary challenges is achieving the necessary peptid...

DeepHLApan: A Deep Learning Approach for the Prediction of Peptide-HLA Binding and Immunogenicity.

Methods in molecular biology (Clifton, N.J.)
Neoantigens are crucial in distinguishing cancer cells from normal ones and play a significant role in cancer immunotherapy. The field of bioinformatics prediction for tumor neoantigens has rapidly developed, focusing on the prediction of peptide-HLA...

Peptidic Compound as DNA Binding Agent: Fragment-based Design, Machine Learning, Molecular Modeling, Synthesis, and DNA Binding Evaluation.

Protein and peptide letters
BACKGROUND: Cancer remains a global burden, with increasing mortality rates. Current cancer treatments involve controlling the transcription of malignant DNA genes, either directly or indirectly. DNA exhibits various structural forms, including the G...

Deep Learning-Assisted Analysis of Immunopeptidomics Data.

Methods in molecular biology (Clifton, N.J.)
Liquid chromatography-coupled mass spectrometry (LC-MS/MS) is the primary method to obtain direct evidence for the presentation of disease- or patient-specific human leukocyte antigen (HLA). However, compared to the analysis of tryptic peptides in pr...

Integrating a Multi-label Deep Learning Approach with Protein Information to Compare Bioactive Peptides in Brain and Plasma.

Methods in molecular biology (Clifton, N.J.)
Peptide therapeutics is gaining momentum. Advances in the field of peptidomics have enabled researchers to harvest vital information from various organisms and tissue types concerning peptide existence, expression and function. The development of mas...

Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity.

Briefings in bioinformatics
Immunologic recognition of peptide antigens bound to class I major histocompatibility complex (MHC) molecules is essential to both novel immunotherapeutic development and human health at large. Current methods for predicting antigen peptide immunogen...

DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning.

Protein science : a publication of the Protein Society
Fungal infections have become a significant global health issue, affecting millions worldwide. Antifungal peptides (AFPs) have emerged as a promising alternative to conventional antifungal drugs due to their low toxicity and low propensity for induci...

Efficient prediction of peptide self-assembly through sequential and graphical encoding.

Briefings in bioinformatics
In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has enabled the effi...

Ionmob: a Python package for prediction of peptide collisional cross-section values.

Bioinformatics (Oxford, England)
MOTIVATION: Including ion mobility separation (IMS) into mass spectrometry proteomics experiments is useful to improve coverage and throughput. Many IMS devices enable linking experimentally derived mobility of an ion to its collisional cross-section...