Laboratory of Bioinformatics and Protein Engineering
International Institute of Molecular and Cell Biology
ul. Ks. Trojdena 4
02-109 Warsaw, Poland
Laboratory of Structural Bioinformatics
Institute of Molecular Biology and Biotechnology
http://bioinformatics.amu.edu.pl Faculty of Biology
Adam Mickiewicz University
http://amu.edu.pl ul. Umultowska 89
61-614 Poznan, Poland
Head of the Laboratory: Janusz M. Bujnicki, PhD, DSc.:
Office: (+48-61) 829-58-39
When using PyRy3D, please cite:
Joanna M. Kasprzak, Mateusz Dobrychłop, Wojciech Potrzebowski, and Janusz M. Bujnicki "PyRy3D: a software tool for modeling of large macromolecular complexes"
JMB and JMK conceived and supervised the study; JMK designed, implemented, tested and benchmarked PyRy3D, designed PyRy3D web server and GUI, MD implemented PyRy3D GUI and performed sf3b modeling, WP and MK helped with implementation of several modules of PyRy3D and tested the program, LP, RN and MS implemented PyRy3D web server under supervision of WR. JMK, MD, WP, MK, WR and JMB wrote the manuscript
The authors thank Grzegorz Chojnowski, Damien Larivière (Fourmentin-Guilbert Foundation) and Dominik Kasprzak for stimulating discussions, testing the program and critical reading of the manuscript. We thank Holger Stark (Max Plank Institute for Biophysical Chemistry), Andrzej Dziembowski (Institute of Biochemistry and Biophysics, Polish Academy of Sciences), Jose Maria Valpuesta (Centro Nacional de Biotecnología), Marcin Nowotny, Wayne Dawson, Stanisław Dunin-Horkawicz, Anna Philips, Katarzyna H. Kaminska, Jarosław Kijek and Radosław Pluta for critical reading of the manuscript. We are also grateful to members of both JMB groups and the participants of the PyRy3D courses and workshops for their help in testing the method and for their feedback. Special thanks go to the first users of PyRy3D and the PyRy3D server for their involvement in the program’s testing.
This analysis was funded by the European Research Council (ERC, StG grant RNA+P=123D to J.M.B.). J.M.K. was additionally supported by the Polish Ministry of Science and Higher Education (MNiSW, grant N N301 123138) and by the National Science Center (NCN, grant 2012/05/N/NZ2/01652). WP was supported by the Foundation for Polish Science (FNP, grant TEAM/2009-4/2 to J.M.B.). J.M.B. was also supported by the “Ideas for Poland” fellowship from the FNP. The development of the webservers in the Bujnicki group was supported by MNiSW (grant POIG.02.03.00–00–003/09 to J.M.B.). Funding for editing of the manuscript was provided by the Ministry of Science and Higher Education of the Republic of Poland, from the quality promoting subsidy, under the Leading National Research Centre (KNOW) programme for the years 2014–2019. Computing resources were provided by IIMCB, by the supercomputer system at the Poznań Supercomputing and Networking Center (grant 98), and by the INterdisc and ICM (grant G56-30).
Components of PyRy3D are based on the following pieces of scientific literature:
 Alber F, Förster F, Korkin D, Topf M, Sali A., Integrating diverse data for structure determination of macromolecular assemblies., Rev Biochem.
 Sali A, Glaeser R, Earnest T, Baumeister W., From words to literature in structural proteomics., Nature.