references.jsonld

{
  "@context": "http://schema.org",
  "@id": "https://github.com/bioexcel/biobb_flexdyn",
  "@type": "ItemList",
  "name": "biobb_flexdyn",
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    {
      "@type": "SoftwareApplication",
      "description": "iMOD is an versatile toolkit to perform Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. Vibrational analysis, motion animations, morphing trajectories and Monte-Carlo simulations can be easily carried out at different scales of resolution using this toolkit.",
      "name": "iMOD",
      "url": "https://chaconlab.org/multiscale-simulations/imod",
      "applicationCategory": "Computational Biology tool",
      "citation": "https://pubmed.ncbi.nlm.nih.gov/21873636/",
      "license": "other",
      "softwareVersion": "1.0.4"
    },
    {
      "@type": "SoftwareApplication",
      "description": "CONCOORD is a method to generate protein conformations around a known structure based on geometric restrictions. Principal component analyses of Molecular Dynamics (MD) simulations of proteins have indicated that collective degrees of freedom dominate protein conformational fluctuations.",
      "name": "CONCOORD",
      "url": "https://www3.mpibpc.mpg.de/groups/de_groot/concoord/",
      "applicationCategory": "Computational Biology tool",
      "citation": "https://pubmed.ncbi.nlm.nih.gov/9329088/",
      "license": "other",
      "softwareVersion": "2.1.2"
    },
    {
      "@type": "SoftwareApplication",
      "description": "NOn-Linear rigid Block NMA approach (NOLB)  a new conceptually simple and computationally efficient method for non-linear normal mode analysis.",
      "name": "NOLB",
      "url": "https://team.inria.fr/nano-d/software/nolb-normal-modes/",
      "applicationCategory": "Computational Biology tool",
      "citation": "https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00197",
      "license": "other",
      "softwareVersion": "1.9"
    },
    {
      "@type": "SoftwareApplication",
      "description": "ProDy is a free and open-source Python package for protein structural dynamics analysis. It is designed as a flexible and responsive API suitable for interactive usage and application development.",
      "name": "ProDy",
      "url": "http://prody.csb.pitt.edu/",
      "applicationCategory": "Computational Biology tool",
      "citation": "https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab187/6211036",
      "license": "https://opensource.org/license/mit",
      "softwareVersion": "2.4.0"
    }
  ]
}