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Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
A deep learning–based tool, Prosit, predicts high-quality peptide tandem mass spectra, improving peptide-identification performance compared with that of traditional proteomics analysis methods. Expand
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Building ProteomeTools based on a complete synthetic human proteome
We describe ProteomeTools, a project building molecular and digital tools from the human proteome to facilitate biomedical research. Here we report the generation and multimodal liquidExpand
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X-ray structure of the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: basis of substrate specificity.
The homodimeric enzyme form of quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa ATCC 17933 crystallizes readily with the space group R3. The X-ray structure was solved at 2.6 AExpand
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A complete substitutional analysis of VIP for better tumor imaging properties
Since numerous tumor cells overexpress the vasoactive intestinal peptide (VIP) receptor subtype 1 (VPAC1), VIP–dye conjugates would be useful as contrast agents for in vivo imaging. However,Expand
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Stepwise transformation of a cholera toxin and a p24 (HIV-1) epitope into D-peptide analogs.
We have transformed two peptide epitopes into D-peptide analogs: VPGSQHIDS derived from cholera toxin recognized by the antibody TE33, and GATPQDLNTML from the HIV-1 capsid protein p24 recognized byExpand
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Evolutionary transition pathways for changing peptide ligand specificity and structure
We identified evolutionary pathways for the inter‐ conversion of three sequentially and structurally unrelated peptides, GATPEDLNQKL, GLYEWGGARI and FDKEWNLIEQN, binding to the same site of theExpand
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ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides*
The analysis of the post-translational modification (PTM) state of proteins using mass spectrometry-based bottom-up proteomic workflows has evolved into a powerful tool for the study of cellularExpand
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Molecular basis for the binding polyspecificity of an anti‐cholera toxin peptide 3 monoclonal antibody
The onset of autoimmune diseases is proposed to involve binding promiscuity of antibodies (Abs) and T‐cells, an often reported yet poorly understood phenomenon. Here, we attempt to approach twoExpand
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Relationships between IgE/IgG4 Epitopes, Structure and Function in Anisakis simplex Ani s 5, a Member of the SXP/RAL-2 Protein Family
Background Anisakiasis is a re-emerging global disease caused by consumption of raw or lightly cooked fish contaminated with L3 Anisakis larvae. This zoonotic disease is characterized by severeExpand
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