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Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry.
Nat Commun. 2022 Oct 6;13(1):5884. doi: 10.1038/s41467-022-33575-4.
Nat Commun. 2022.
PMID: 36202813
Free PMC article.
Dockground: A comprehensive data resource for modeling of protein complexes.
Kundrotas PJ, Anishchenko I, Dauzhenka T, Kotthoff I, Mnevets D, Copeland MM, Vakser IA.
Kundrotas PJ, et al. Among authors: dauzhenka t.
Protein Sci. 2018 Jan;27(1):172-181. doi: 10.1002/pro.3295. Epub 2017 Oct 10.
Protein Sci. 2018.
PMID: 28891124
Free PMC article.
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Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking.
Dauzhenka T, Kundrotas PJ, Vakser IA.
Dauzhenka T, et al.
J Comput Chem. 2018 Sep 15;39(24):2012-2021. doi: 10.1002/jcc.25381. Epub 2018 Sep 18.
J Comput Chem. 2018.
PMID: 30226647
Free PMC article.
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Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.
Kundrotas PJ, Anishchenko I, Badal VD, Das M, Dauzhenka T, Vakser IA.
Kundrotas PJ, et al. Among authors: dauzhenka t.
Proteins. 2018 Mar;86 Suppl 1(Suppl 1):302-310. doi: 10.1002/prot.25380. Epub 2017 Sep 28.
Proteins. 2018.
PMID: 28905425
Free PMC article.
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Application of docking methodologies to modeled proteins.
Singh A, Dauzhenka T, Kundrotas PJ, Sternberg MJE, Vakser IA.
Singh A, et al. Among authors: dauzhenka t.
Proteins. 2020 Sep;88(9):1180-1188. doi: 10.1002/prot.25889. Epub 2020 Mar 20.
Proteins. 2020.
PMID: 32170770
Free PMC article.
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