Clustering molecular dynamics conformations of the CC’-loop of the PD-1 immuno-checkpoint receptor Article Swipe
Wolfgang Schreiner
,
Rudolf Karch
,
Michael Cibena
,
Lisa Tomasiak
,
Michael Kenn
,
Georg Pfeiler
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1016/j.csbj.2023.07.004
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1016/j.csbj.2023.07.004
Molecular mechanisms within the checkpoint receptor PD-1 are essential for its activation by PD-L1 as well as for blocking such an activation via checkpoint inhibitors. We use molecular dynamics to scrutinize patterns of atomic motion in PD-1 without a ligand. Molecular dynamics is performed for the whole extracellular domain of PD-1, and the analysis focuses on its CC'-loop and some adjacent Cα-atoms. We extend previous work by applying common nearest neighbor clustering (Cnn) and compare the performance of this method with Daura clustering as well as UMAP dimension reduction and subsequent agglomerative linkage clustering. As compared to Daura clustering, we found Cnn less sensitive to cutoff selection and better able to return representative clusters for sets of different 3D atomic conformations. Interestingly, Cnn yields results quite similar to UMAP plus linkage clustering.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1016/j.csbj.2023.07.004
- http://www.csbj.org/article/S2001037023002386/pdf
- OA Status
- gold
- Cited By
- 1
- References
- 44
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4384207092
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- OpenAlex ID
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https://openalex.org/W4384207092Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1016/j.csbj.2023.07.004Digital Object Identifier
- Title
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Clustering molecular dynamics conformations of the CC’-loop of the PD-1 immuno-checkpoint receptorWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-01-01Full publication date if available
- Authors
-
Wolfgang Schreiner, Rudolf Karch, Michael Cibena, Lisa Tomasiak, Michael Kenn, Georg PfeilerList of authors in order
- Landing page
-
https://doi.org/10.1016/j.csbj.2023.07.004Publisher landing page
- PDF URL
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https://www.csbj.org/article/S2001037023002386/pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.csbj.org/article/S2001037023002386/pdfDirect OA link when available
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Molecular dynamics, Cluster analysis, Loop (graph theory), Dynamics (music), Chemistry, Computational biology, Biophysics, Physics, Biological system, Computer science, Biology, Computational chemistry, Mathematics, Combinatorics, Artificial intelligence, AcousticsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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1Total citation count in OpenAlex
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2025: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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