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

doi:10.1016/j.xpro.2023.102682

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

STAR Protoc. 2023 Dec 15;4(4):102682. doi: 10.1016/j.xpro.2023.102682. Epub 2023 Nov 18.

Authors

Yu Yan¹, Dean Wang², Ruiqi Xin³, Raine A Soriano⁴, Dominic C M Ng², Wei Wang⁵, Peipei Ping⁶

Affiliations

¹ 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.
² 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.
³ Computational and Systems Biology Interdepartmental Program (IDP), University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA.
⁴ Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA.
⁵ 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.
⁶ 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. Electronic address: pping38@g.ucla.edu.

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.

Keywords: Bioinformatics; Computer Sciences; Protein Biochemistry; Sequence Analysis.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Amino Acids*
Humans
Protein Processing, Post-Translational* / genetics

Substances

Amino Acids

Abstract

Publication types

MeSH terms

Substances

Grants and funding