ProDy

ProDy is a software tool to perfom analysis of structural dynamics and sequences of proteins. The ProDy tool package includes user-defined atom selections for contact identification and structure comparisons. The algorithm can use heterogeneous X-ray structures, mixed structural datasets from a Blast search, NMR models, and MD snapshots for principa component analysis (PCA). The 'normal' mode analyses use the Anisotropic network model (ANM), Gaussian network model (GNM), and ANM/GNM with distance and property-dependent force constants. Users can implement new methods using the ProDy API.

Topic

Protein structure analysis;Sequence analysis

Detail

  • Operation: Protein structure analysis

  • Software interface: Command-line user interface

  • Language: Python

  • License: The MIT licence

  • Cost: Free

  • Version name: v2.x

  • Credit: National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: Ivet Bahar bahar@pitt.edu

  • Collection: -

  • Maturity: Mature

Publications

  • ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python
  • Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. Bioinformatics. 2021 Apr 5;37(20):3657–9. doi: 10.1093/bioinformatics/btab187. Epub ahead of print. PMID: 33822884; PMCID: PMC8545336.
  • https://doi.org/10.1093/bioinformatics/btab187
  • PMID: 33822884
  • PMC: PMC8545336
  • ProDy: protein dynamics inferred from theory and experiments.
  • Bakan A, Meireles LM, Bahar I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics. 2011 Jun 1;27(11):1575-7. doi: 10.1093/bioinformatics/btr168. Epub 2011 Apr 5. PMID: 21471012; PMCID: PMC3102222.
  • https://doi.org/10.1093/bioinformatics/btr168
  • PMID: 21471012
  • PMC: PMC3102222
  • Evol and ProDy for bridging protein sequence evolution and structural dynamics
  • Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I. Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics. 2014 Sep 15;30(18):2681-3. doi: 10.1093/bioinformatics/btu336. Epub 2014 May 21. PMID: 24849577; PMCID: PMC4155247.
  • https://doi.org/10.1093/bioinformatics/btu336
  • PMID: 24849577
  • PMC: PMC4155247

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