ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics, 2021•academic.oup.com
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 …
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 …
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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