AIMC Topic: Peptide Library

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Deep Learning-Based Prediction of Decoy Spectra for False Discovery Rate Estimation in Spectral Library Searching.

Journal of proteome research Apr 19, 2025
With the advantage of extensive coverage, predicted spectral libraries are becoming an attractive alternative in proteomic data analysis. As a popular false discovery rate estimation method, target decoy search has been adopted in library search work...
Proteomics Databases, Protein Tandem Mass Spectrometry Deep Learning Peptide Library
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A new strategy to HER2-specific antibody discovery through artificial intelligence-powered phage display screening based on the Trastuzumab framework.

Biochimica et biophysica acta. Molecular basis of disease Mar 7, 2025
Human epidermal growth factor receptor 2 (HER2) is a recognized drug target, and it serves as a critical target for various cancer treatments, necessitating the discovery of more antibodies for therapeutic and detection purposes. Here, we have develo...
Trastuzumab Peptide Library Cell Surface Display Techniques Receptor, ErbB-2 Humans Artificial Intelligence
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An antibody developability triaging pipeline exploiting protein language models.

mAbs Mar 4, 2025
Therapeutic monoclonal antibodies (mAbs) are a successful class of biologic drugs that are frequently selected from phage display libraries and transgenic mice that produce fully human antibodies. However, binding affinity to the correct epitope is n...
Peptide Library Antibodies, Monoclonal Animals Mice Humans Machine Learning
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Unveiling the new chapter in nanobody engineering: advances in traditional construction and AI-driven optimization.

Journal of nanobiotechnology Feb 6, 2025
Nanobodies (Nbs), miniature antibodies consisting solely of the variable region of heavy chains, exhibit unique properties such as small size, high stability, and strong specificity, making them highly promising for disease diagnosis and treatment. T...
Artificial Intelligence Animals Humans Protein Engineering Cell Surface Display Techniques Peptide Library Single-Domain Antibodies
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Nanobody screening and machine learning guided identification of cross-variant anti-SARS-CoV-2 neutralizing heavy-chain only antibodies.

PLoS pathogens Jan 23, 2025
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to persist, demonstrating the risks posed by emerging infectious diseases to national security, public health, and the economy. Development of new vaccines and antibodies for emer...
Immunoglobulin Heavy Chains Spike Glycoprotein, Coronavirus Antibodies, Neutralizing High-Throughput Screening Assays Single-Domain Antibodies Peptide Library Antibodies, Viral SARS-CoV-2 Animals Machine Learning COVID-19 Humans
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Feature selection enhances peptide binding predictions for TCR-specific interactions.

Frontiers in immunology Jan 23, 2025
INTRODUCTION: T-cell receptors (TCRs) play a critical role in the immune response by recognizing specific ligand peptides presented by major histocompatibility complex (MHC) molecules. Accurate prediction of peptide binding to TCRs is essential for a...
Peptides Protein Binding Machine Learning Receptors, Antigen, T-Cell Peptide Library Animals Mice
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Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds.

PLoS computational biology Nov 18, 2024
Peptides are an emerging modality for developing therapeutics that can either agonize or antagonize cellular pathways associated with disease, yet peptides often suffer from poor chemical and physical stability, which limits their potential. However,...
Machine Learning Peptides Disulfides Peptide Library Models, Molecular Protein Folding Amino Acid Sequence Computational Biology
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Beyond Natural Immune Repertoires: Synthetic Antibodies.

Cold Spring Harbor protocols Apr 1, 2024
Synthetic antibody libraries, in which the antigen-binding sites are precisely designed, offer unparalleled precision in antibody engineering, exceeding the potential of natural immune repertoires and constituting a novel generation of research tools...
Antibodies Antigens Artificial Intelligence Peptide Library
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Merging Full-Spectrum and Fragment Ion Intensity Predictions from Deep Learning for High-Quality Spectral Libraries.

Journal of proteome research Nov 1, 2023
Spectral libraries are useful resources in proteomic data analysis. Recent advances in deep learning allow tandem mass spectra of peptides to be predicted from their amino acid sequences. This enables predicted spectral libraries to be compiled, and ...
Deep Learning Software Peptide Library Peptides Proteomics Databases, Protein
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PepScaf: Harnessing Machine Learning with In Vitro Selection toward De Novo Macrocyclic Peptides against IL-17C/IL-17RE Interaction.

Journal of medicinal chemistry Jul 22, 2023
The combination of library-based screening and artificial intelligence (AI) has been accelerating the discovery and optimization of hit ligands. However, the potential of AI to assist in de novo macrocyclic peptide ligand discovery has yet to be full...
Interleukin-17 Artificial Intelligence Peptide Library Machine Learning Peptides
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