Protocol for the prediction, interpretation, and mutation evaluation of post-translational modification using MIND-S

Yu Yan; Dean Wang; Ruiqi Xin; Raine A. Soriano; Dominic C.M. Ng; Wei Wang; Peipei Ping

STAR Protocols (Dec 2023)

Protocol for the prediction, interpretation, and mutation evaluation of post-translational modification using MIND-S

Yu Yan,
Dean Wang,
Ruiqi Xin,
Raine A. Soriano,
Dominic C.M. Ng,
Wei Wang,
Peipei Ping

Affiliations

Yu Yan: NIH 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
Dean Wang: NIH 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; Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA
Ruiqi Xin: Computational and Systems Biology Interdepartmental Program (IDP), University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA
Raine A. Soriano: Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA
Dominic C.M. Ng: NIH 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; Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA
Wei Wang: Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA; Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA
Peipei Ping: NIH 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; Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA; Department of Medicine (Cardiology), UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA; Corresponding author

Journal volume & issue: Vol. 4, no. 4
p. 102682

Abstract

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Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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