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

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)...

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Autores principales: Zhang, She, Krieger, James M, Zhang, Yan, Kaya, Cihan, Kaynak, Burak, Mikulska-Ruminska, Karolina, Doruker, Pemra, Li, Hongchun, Bahar, Ivet
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8545336/
https://www.ncbi.nlm.nih.gov/pubmed/33822884
http://dx.doi.org/10.1093/bioinformatics/btab187
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author Zhang, She
Krieger, James M
Zhang, Yan
Kaya, Cihan
Kaynak, Burak
Mikulska-Ruminska, Karolina
Doruker, Pemra
Li, Hongchun
Bahar, Ivet
author_facet Zhang, She
Krieger, James M
Zhang, Yan
Kaya, Cihan
Kaynak, Burak
Mikulska-Ruminska, Karolina
Doruker, Pemra
Li, Hongchun
Bahar, Ivet
author_sort Zhang, She
collection PubMed
description 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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spelling pubmed-85453362021-10-26 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 Bioinformatics Applications Notes 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. Oxford University Press 2021-04-05 /pmc/articles/PMC8545336/ /pubmed/33822884 http://dx.doi.org/10.1093/bioinformatics/btab187 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Zhang, She
Krieger, James M
Zhang, Yan
Kaya, Cihan
Kaynak, Burak
Mikulska-Ruminska, Karolina
Doruker, Pemra
Li, Hongchun
Bahar, Ivet
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
title ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
title_full ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
title_fullStr ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
title_full_unstemmed ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
title_short ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
title_sort prody 2.0: increased scale and scope after 10 years of protein dynamics modelling with python
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8545336/
https://www.ncbi.nlm.nih.gov/pubmed/33822884
http://dx.doi.org/10.1093/bioinformatics/btab187
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