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ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.
Zhang, She; Krieger, James M; Zhang, Yan; Kaya, Cihan; Kaynak, Burak; Mikulska-Ruminska, Karolina; Doruker, Pemra; Li, Hongchun; Bahar, Ivet.
Afiliación
  • Zhang S; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
  • Krieger JM; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
  • Zhang Y; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
  • Kaya C; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
  • Kaynak B; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
  • Mikulska-Ruminska K; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
  • Doruker P; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
  • Li H; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
  • Bahar I; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
Bioinformatics ; 37(20): 3657-3659, 2021 Oct 25.
Article en En | MEDLINE | ID: mdl-33822884
SUMMARY: ProDy, an integrated application programming interface developed for modelling and analysing protein dynamics, has significantly evolved in recent years in response to the growing data and needs of the computational biology community. We present major developments that led to ProDy 2.0: (i) improved interfacing with databases and parsing new file formats, (ii) SignDy for signature dynamics of protein families, (iii) CryoDy for collective dynamics of supramolecular systems using cryo-EM density maps and (iv) essential site scanning analysis for identifying sites essential to modulating global dynamics. AVAILABILITY AND IMPLEMENTATION: ProDy is open-source and freely available under MIT License from https://github.com/prody/ProDy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido