Evidence map›Paper›PMID 42056699›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

MD-Phylogeny: Constructing Statistically Supported Phylogenetic Trees from Protein Structures Using Molecular Dynamics.

Désirée B Langer, Ashar J Malik, Paul Klemm, Jane R Allison, Anthony M Poole

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Article in Methods in molecular biology (Clifton, N.J.), 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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0citing papers in PubMed
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1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Désirée B LangerSchool of Biological Sciences, The University of Auckland, Auckland, New Zealand.
Ashar J MalikSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
Paul KlemmCenter for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
Jane R AllisonSchool of Biological Sciences, The University of Auckland, Auckland, New Zealand.
Anthony M PooleSchool of Biological Sciences, The University of Auckland, Auckland, New Zealand. a.poole@auckland.ac.nz.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Phylogenetic tree construction from homologous sequences is a fundamental approach for studying evolutionary relationships. However, in cases where sequence similarity is too low to generate reliable alignments, comparison of protein structure provides an alternative means for inferring deep evolutionary relationships. MD-phylogeny is a method that integrates structural comparison with molecular dynamics (MD) simulations to generate robust phylogenies for protein datasets within the twilight zone of sequence similarity. This approach uses well-established structural superposition methods for building trees from structure, with a method for generating structural variants using MD simulations, from which confidence scores analogous to bootstrapping can be derived.This protocol provides a step-by-step guide to performing MD-phylogeny, covering dataset selection, structural comparisons, tree construction, and the generation of statistical support through MD simulations.

Indexed as

Computational BiologyMolecular Dynamics SimulationPhylogenyProteinsEvolution, MolecularProtein ConformationProteinsEvolutionMolecular dynamicsProtein structureStructural phylogenyTwilight zone

Identifiers

PMID42056699

What OpenQuestion holds

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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.