Open AccessProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
Author(s) -
She Zhang,
James Krieger,
Yan Zhang,
Cihan Kaya,
Burak Kaynak,
Karolina MikulskaRuminska,
Pemra Doruker,
Hongchun Li,
İvet Bahar
Publication year - 2021
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btab187
Subject(s) - python (programming language) , computer science , interfacing , mit license , scope (computer science) , parsing , open source , license , file format , programming language , software , operating system , computer hardware
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.