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ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.

ABSTRACT:

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.

SUBMITTER: Zhang S

PROVIDER: S-EPMC8545336 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.

Zhang She S Krieger James M JM Zhang Yan Y Kaya Cihan C Kaynak Burak B Mikulska-Ruminska Karolina K Doruker Pemra P Li Hongchun H Bahar Ivet I

Bioinformatics (Oxford, England) 20211001 20

<h4>Summary</h4>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 c ...[more]

PMID: 33822884

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