Dokholyan Group

Dokholyan group is from Department of Pharmacology, Penn State College of Medicine, Hershey, USA.
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Publications:

  1. Ding F, Sharma S, Chalasani P, Demidov VV, Broude NE, Dokholyan NV. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA. 2008 Jun;14(6):1164-73.
  2. Sharma S, Ding F, Dokholyan NV. iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics. 2008 Sep 1;24(17):1951-2.
  3. Krokhotin A, Houlihan K, Dokholyan NV. iFoldRNA v2: folding RNA with constraints. Bioinformatics. 2015 Sep 1;31(17):2891-3.
  4. Wang J, Williams B, Chirasani VR, Krokhotin A, Das R, Dokholyan NV. Limits in accuracy and a strategy of RNA structure prediction using experimental information. Nucleic Acids Res. 2019 Jun 20;47(11):5563-5572.
  5. Sha CM, Wang J, Dokholyan NV. Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks. Biophys J. 2023 Oct 14:S0006-3495(23)00647-1.
  6. Proctor, Elizabeth A., Feng Ding, and Nikolay V. Dokholyan. Discrete molecular dynamics. Wiley Interdisciplinary Reviews: Computational Molecular Science 1.1 (2011): 80-92.