Protocol for the prediction, interpretation, and mutation evaluation of post-translational modification using MIND-S
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Updated: Jul 10, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
Yu Yan1, Dean Wang2, Ruiqi Xin3
1NIH BRIDGE2AI Center at UCLA & NHLBI Integrated Cardiovascular Data Science Training Program at UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA; Medical Informatics Program, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA; Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA.
Abstract:
Post-translational modifications (PTMs) serve as key regulatory mechanisms in various cellular processes; altered PTMs can potentially lead to human diseases. We present a protocol for using MIND-S (multi-label interpretable deep-learning approach for PTM prediction-structure version), to study PTMs. This protocol consists of step-by-step guide and includes three key applications of MIND-S: PTM predictions based on protein sequences, important amino acids identification, and elucidation of altered PTM landscape resulting from molecular mutations. For complete details on the use and execution of this protocol, please refer to Yan et al (2023).1.
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