People
- Development Team
- Contributors

Release Notes

v2.5.0 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

People¶

ProDy is being developed in the Bahar Lab at the University of Pittsburgh with support from NIH R01 GM099738 award.

Development Team¶

Ahmet Bakan initiated the ProDy project, designed and developed ProDy, NMWiz, Evol, and DruGUI.

Cihan Kaya was overseeing the overall development of ProDy from 2015 to 2018.

She (John) Zhang was helping with maintaining and developing ProDy from 2016, and took on the overseeing role from 2018 to mid 2020.

James Krieger was helping develop ProDy from 2017 and became the main overseer and developer in mid 2020.

Hongchun Li has helped maintain and develop ANM and GNM servers, and made significant contributions to database and dynamics including SignDy and Adaptive ANM.

JiYoung Lee is the main developer of Pharmmaker, for constructing pharmacophore models using the outputs from DruGUI.

Yan Zhang contributed significantly to the development of the cryo-EM module, protein.emdmap.

Burak Kaynak contributed significantly to the development of domain_decomposition, dynamics.essa, and dynamics.clustenm.

Karolina Mikulska-Ruminska is one of the main developers since 2022, with the addition of the new modules protein.interactions (InSty), protein.waterbridges (WatFinder), in addition to being the developer of dynamics.mechstiff (MechStiff).

Anthony Bogetti is overseeing the overall development of ProDy since 2024.

Anindita Dutta contributed to the development of Evol, database and sequence modules.

Tim Lezon contributed to development of Rotations and Translation of Blocks and Membrane ENM.

Wenzhi Mao contributed to development of MSA analysis functions.

Lidio Meireles provided insightful comments on the design of ProDy, and contributed to the development of ProDy Applications.

Mustafa Tekpinar contributed to the development of MechStiff.

Luca Ponzoni contributed to the development of SignDy.

David Koes contributed to the development of drug discovery tools.

Contributors¶

In addition to the development team members, we acknowledge contributions and feedback from the following individuals:

Ying Liu provided the code for Perturbation Response Scanning method.

Frane Doljanin provided the code for the water bridge detection.

Kian Ho contributed with bug fixes and unit tests for DSSP functions.

Gökçen Eraslan contributed with bug fixes and development and maintenance insights.