<i>ProDy</i> 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
She Zhang, James Krieger, Yan Zhang, Cihan Kaya, Burak Kaynak, Karolina Mikulska‐Ruminska, Pemra Doruker, Hongchun Li, İvet Bahar
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.