Molecular Dynamics Simulation and Docking of MUC1 O-Glycopeptide.

Ryoka Kokubu, Shiho Ohno, Noriyoshi Manabe, Yoshiki Yamaguchi

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Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

4 authors.

Ryoka KokubuDivision of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan.

Shiho OhnoDivision of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan.

Noriyoshi ManabeDivision of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan.

Yoshiki YamaguchiDivision of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan. yyoshiki@tohoku-mpu.ac.jp.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Advances in computer performance and computational simulations allow increasing sophistication in applications in biological systems. Molecular dynamics (MD) simulations are especially suitable for studying conformation, dynamics, and interaction of flexible biomolecules such as free glycans and glycopeptides. Computer simulations are best performed when the scope and limitations in performance have been thoroughly assessed. Proper outputs are obtained only under suitable parameter settings, and results need to be properly validated. In this chapter, we will introduce an example of molecular dynamics simulations of MUC1 O-glycopeptide and its docking to anti-MUC1 antibody Fv fragment.

Indexed as

Molecular Dynamics SimulationMucin-1Antibodies, MonoclonalGlycopeptidesMolecular ConformationMolecular Docking SimulationAntibodies, MonoclonalGlycopeptidesMucin-1AntibodyDocking simulationGlycopeptideHomology modelingMD simulationMUC1

Identifiers

PMID38347427

DOI10.1038/s41586-021-03819-2

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.