Computational Investigation of GNMT-Catalyzed Methyl Transfer Reaction: Integrating MD, QM, and ML Approaches.

Jonathan Epih, Anjali Arya, Saghar Gomrok, Qianyi Cheng

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Article in Journal of computational chemistry, 2026. 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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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

4 authors.

Jonathan EpihDepartment of Chemistry, University of Memphis, Memphis, Tennessee, USA.

Anjali AryaDepartment of Chemistry, University of Memphis, Memphis, Tennessee, USA.

Saghar GomrokDepartment of Chemistry, University of Memphis, Memphis, Tennessee, USA.ORCID https://orcid.org/0009-0004-6359-7438

Qianyi ChengDepartment of Chemistry, University of Memphis, Memphis, Tennessee, USA.ORCID https://orcid.org/0000-0002-4640-2238

Funding

Data Mining and Machine Learning Guided QM/MM and QM-Cluster Modeling of Enzymatic ReactionsR35GM145206 · NIGMS · UNIVERSITY OF MEMPHIS · PI Qianyi Cheng · 2022 to 2026

$1.6M

National Institute of General Medical Sciences of the National Institutes of Health 1R35GM145206NIGMS NIH HHS R35 GM145206

6 · The paper itself

Abstract

The glycine N-methyltransferase (GNMT) reaction was examined using an integrated workflow combining molecular dynamics (MD), quantum mechanical (QM) cluster calculations, and machine learning (ML) analysis. Instead of relying on a single crystal-like conformation, multiple MD simulations were used to sample diverse reactant (SAM + glycine bound to GNMT) and product (SAH + sarcosine bound to GNMT) state geometries for QM cluster modeling. Across more than 150 QM-cluster models constructed by the Residue Interaction Network ResidUe Selector (RINRUS) from selected MD frames with and without explicit waters, the computed activation and reaction free energies span broad ranges (7 to 25 kcal mol

Indexed as

enzyme catalysismachine learningmethyl‐transfermolecular dynamicsQM‐cluster modeling

Identifiers

PMID42252606

DOI10.1002/jcc.70434

PMCPMC13312424

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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.