PyRy3D - Users opinions

We would like to encourage our users to give us a feedback about PyRy3D software. If you have ever:

  • tried PyRy3D for modeling
  • attended any of our workshops or seen a presentation about the software
  • found this page and read the program description

Please contact us directly and give us feedback :-) We will be happy to improve the software and adjust it to your needs!

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You can read about PyRy3D and models generated with it in the following publications:

  • Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski L, Dunin-Horkawicz S, Bujnicki JM, Computational modeling of protein-RNA complex structures, Methods 2013 Sep 29. doi:pii: S1046-2023(13)00383-6. 10.1016/j.ymeth.2013.09.014.

  • Dzananovic E, Patel TR, Chojnowski G, Boniecki MJ, Deo S, McEleney K,Harding SE, Bujnicki JM, McKenna SA, Solution conformation of Adenovirus Virus Associated RNA-I and its interaction with PKR, J Struct Biol 2014 Jan;185(1):48-57. doi: 10.1016/j.jsb.2013.11.007. [Epub 2013 Nov 28 2013]


Here are some recommendations we have already received:

  • Dariusz Plewczynski, Fulbright visiting professor, The Jackson Laboratory for Genomic Medicine & Yale University & Interdisciplinary Centre  for Mathematical and Computational Modelling; University of Warsaw

    PyRy3D allows for modeling of macromolecular complexes similarly as one can build very complex structures using simple lego bricks. In my case, I am interested in modeling of three-dimensional structure of chromatin for selected regions for human genome. Because of the complexity of the problem, in my case the crucial point is to have the access to source code, which will be provided when the paper will be published. Until than I am using the web sever which provides full functionality of the program.

    Overall, I am very impressed by the quality of the software, and its speed. The web server is working without any glitches, providing rapidly results with the proper description. The visualization is integrated with UCSF Chimera, which provides very easy interface for the whole hybrid modeling platform implemented in PyRy3D. Authors are very friendly, professional and helpful. The optimized version using GPU is excellent, providing the significant advancement in comparison to other methods, or previous versions of the software.
  • Pedro Fernandes, experienced bioinformatics trainer and training course designer.The “Gulbenkian Training Programme in Bioinformatics”, GTPB, since 1999, at Instituto Gulbenkian de Ciência, Oeiras, Portugal

    The PyRy3d software is a unique tool in many aspects. Unlike the majority of the available open source tools for similar purposes, that are rigid designs, PyRy3d offers a complete yet fully configurable modeling platform, suitable for large macromolecular complexes for which structure determination is not only a heavy computational task, it is a computationally difficult problem. PyRy3d offers numerous possibilities of using Monte Carlo simulation techniques to approximate biomolecular structures while employing experimental results from NMR spectroscopy, SAXS, Crio-EM, etc., not only as constraints to confine the space of solutions, but also as criteria to evaluate and optimise model quality. Exploration of the space of solutions is made where it matters and convergence takes valuable experimental data into consideration.

    PyRy3d is a very robust software platform, well documented and user friendly. As far as I am concerned, as a training course designer, organiser and facilitator, I was delighted to participate in the genesis and actual delivery of the SMLMC14 training course in Portugal (GTPB, June 2014). Here I could see how scientists with a wide range of backgrounds could adapt to the new simulation and structure determination platform easily via hands-on training, in about 20 hours. The training component was developed on purpose for this course and revealed itself as an easy way to reach usability, gain self-confidence and autonomy (user independence). This is a value that is difficult to replace with self-tuition, as the learning curve in a well designed course rapidly becomes steep and the interaction with competent instructors is an opportunity to overcome usage difficulties at a very early stage, as the need arises.

    The PyRy3d development team has correctly decided to step in to better usability by incorporating it as a module of the open source UCSF Chimera visualisation package, instead of developing yet another proprietary GUI. This way a PyRy3d analysis can be comfortably launched from within the Chimera environment.

    On the other hand, the implementation in a publicly available server was also a correct move towards reliable service provision, especially suitable for large scale computational loads that can easily emerge as addressing problems of higher structural complexity.

    I am pretty sure that PyRy3d is here to stay, not only for its own merits as an analytical platform, but because it represents an innovative way of integrating experimental data very cleverly into the mechanisms of model refinement. The ideas behind the design can be ported into other areas of macromolecular structural determination by numerical approximation.
  • Satyavati Kharde PhD student, Biochemistry centre, Heidelberg University, Germany:

    I find PyRy3D as a very rare and useful program/server. Most of my work involves integration of various structural information be it X-ray or cross linking from mass spectrometry. Many a times, it is difficult to put together all the data and interpret some sense out of it. PyRy3D helps to ease the integration and record the simulations that runs in it. One Fascination feature amongst many is the ranking and assessment of models it generates. I was introduced to this program in a structural modelling course.
  • Charles Winterhalter PhD student, Newcastle University, ICO2S research group, England:

    I have discovered Pyry3D during the Structural Modelling for Large Molecular Complexes workshop and was demonstrated with direct application for real biological data. The software itself uses a Monte-Carlo approach, which allows for more flexibility in simulations and results concordance with experimental data. The Chimera plugin extension provides a wide range of visualisation tools, and is especially worth for validation while using the clustering method with models generated via Pyry3D. Power of the tool goes beyond standard methods for 3D-visualisation of biological macrocomplexes and is quite straightforward to use. I strongly recommend Pyry3D to anyone who would like a good prediction pipeline for producing low-resolution models.
  • Virginie Martiny PhD, Molecular Modelling and Structural Crystallography Institut de Chimie des Substances Naturelles CNRS UPR 2301, LabEx LERMIT, France:

    I attended the SMLMC14 workshop in order to learn more about PyRy3D. As a part of my research project, I was interested in finding a tool capable of dealing with large macromolecular complexes and electronic map density. During the practical sessions, I discovered how PyRy3D is user friendly and powerful. More importantly, I really appreciated the possibility to tune all parameters. I intend to use it soon on my own data. To finish, I also have to say that the authors of PyRy3D are very helpful and reactive.
  • Diogo Santos-Martins,PhD student, REQUIMTE, Department of Chemistry and Biochemistry, University of Porto, Portugal

    I learned about PyRy3D in a workshop and appreciated how it provides intuitive usage while keeping things versatile. It is easy to change the scoring function and conformational search parameters in order to tune the program for specific problems.
  • Silvana Pompeia Univ. Estadual Paulista, Brazil

    Thanks very much! The course (in Oeiras, Portugal, lead by PyRy3D developer) was excellent! I found the program very easy to use and generating very promising results. I intend to use the PyRy3D in my research because this is excelent tool for bioinformatics.
  • Mateusz Koryciński PhD student, the Department of Protein Evolution, Max-Planck Institute for Developmental Biology, Tübingen, Germany:

    PyRy3D allowed me to propose a model of a macromolecular complex consisting of many different components. Implemented algorithm performed very well and simulations returned results of a very good quality. Possibility to cluster and score resulting decoys significantly simplified the whole process, especially analysis of the data. One of the great advantages of the software is graphical user interface working as an UCSF Chimera extension. It allows in a simple way to control parameters of the simulation, as well as analyze and visualize the results. Authors were very helpful in case of any problems concerning installation and modelling process. I would recommend this tool to anyone who is looking for a fast and reliable way to model complex systems.

  • Michał Taube PhD student, Adam Mickiewicz University in Poznan:

    I learned about PyRy3D during the SMLMC14 course at the Instituto Gulbenkian de Ciência given by the author of the PyRy3D - Joanna Kasprzak, PhD and Grzegorz Chojnowski, PhD. The lectures covered very broad range of topics from experimental to bioinformatics techniques for the determination of the structure of proteins and nucleic acids. During very interesting practical sessions we learned how to model protein and RNA structures and what was more important how to use and what offers the PyRy3D software.
    I am working daily with the saxs data and I found that user friendly interface and possibility to customize settings within the modeling software is very important and sometimes it is crucial for the successful modeling especially in case of protein complexes. PyRy3D as a server and stand-alone program meets all this expectations. First of all it can fit macromolecular structure in to the density maps with addition of the experimentally determined restrains. This option is very useful in case of fitting the structures into the density map from the electron microscopy. At the same time PyRy3D allows modeling of the structure taking into account fit to the saxs scattering curve or pair distance distribution function. Additional futures like clustering of the models, modeling of the flexible parts of the proteins and UCSF Chimera plug-in makes PyRy3D even more powerful. I can truly recommend PyRy3D to anyone who works with saxs or electron microscopy data !!!

  • Krzysztof Kus PhD student, Instituto Gulbenkian de Ciencia:

    I had a pleasure to be introduced to PyRy3D software during Structural Modelling for Large Macromolecular Complexes course held in Oeiras, Portugal. I reckon that this is a great piece of software which enables to integrate many types of experimental information (X-ray, SAXS, FRET etc.) to create the best model which explain the available data. Beside this it also enables to deal with parts where structural data is missing. I think that PyRy3D is user friendly and well documented which means that people starting to work with it, they should not encounter any difficulties with studying their complex of interest. Moreover it includes routines for clustering of created models and preparations of the movies. I hope to have opportunity to use this software in my research.

  • Damien Lariviere PhD, Fourmentin-Guilbert Scientific Foundation:

    I took contact with PyRy3D developers because I needed a tool to predict macromolecular assemblies from experimental data in an intuitive and reproducible manner. I thus tested PyRy3D as an extension for UCSF Chimera. It is really made for researchers non expert in simulation but willing to make sense of low-resolution spatial data from EM, chemical cross-linking or FRET. The interface drives the user from the preparation of the simulation to the ranking of the solutions. Clustering the models is still missing but the imminent implementation of this important task should make PyRy3D a key tool in the data-driven, reproducible process leading to propose relevant configurations of proteins into complexes. I appreciate the tool to be supported by a lab giving reactive support, visibility and durability.

  • Grzegorz Chojnowski PhD, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw:

    I’ve used PyRy3D in two projects. First was a relatively simple semi-flexible fitting of a RNA model into ab initio SAXS reconstruction. Second was a bit more difficult since a protein-RNA complex was fitted into two complementary SAXS reconstructions – one for each part of the complex. Furthermore the protein component had two domains connected with a flexible linker. In both cases Pyry3D produced satisfactory and reproducible results. I must admit that initially I was a bit scared by the number of parameters required by the program. PyRy3D, however, turned out to be very easy to learn and I found using it real fun. Mostly owing its speed and huge convergence radius.

  • Tomasz Woźniak, PhD student, Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań:

    I took part in the PyRy 3D workshop during SocBiN2013 in Toruń. The workshop was very interesting and explained crucial PyRy3D functionalities. Presented tool allows to dock known structures into an electron density map allowing user to select main parameters steering this procedure. This functionality may be very useful if experimental data describing complex are available. What I found really important is the fact, that PyRy3D can successfully dock many molecules in the same time. This program can also take into account regions for which no structural data are available. Program is very intuitive and can be run through UCSF Chimera interface. Clear results visualization allows a user to check results in the short time. I may use this software in future projects.

  • Katarzyna Kulinska, PhD, Department of Bioinformatics, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań:

    PyRy3D software seems to be very useful tool to predict 3D structures of macromolecular complexes. It allows effective application of different kind of experimental information (from X-ray, NMR, FRET, EM, chemical cross-linking etc) to built and study structural models. It may also include regions for which no structural data are available. The graphical user interface embedded as an UCSF Chimera extension is useful and intuitive. Presented at the PyRy3D workshop during SocBiN2013 in Toruń examples of applications showed that the algorithm perform very well and simulations return results of a good quality. The workshop presentation clearly explained PyRy3D functionalities, was very interesting and professional. I appreciate this tool and plan to use this software in my lab.

  • Małgorzata Szeląg, PhD student, at Department of Human Molecular Genetics, Adam Mickiewicz University, Poznań:

    I had a possibility to acquaint myself with PyRy3D software during the workshop organized on SocBin Conference in Toruń. I am a person who feel comfortable working on programs with graphical interface (GUI). And PyRy3D is one of them. I plan to use it for my projects as soon as I have all protein structures of a complex of my interest. The program is simple in use and nicely written manual helps a lot. I also like the idea of combining PyRy3D with free UCSF Chimera viewer. I strongly encourage authors to develop this bioinformatic tool further.

  • Anna Czerwoniec, PhD, Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University

    Together with PyRy3D developer I managed to assemble a structure of macromolecular complex I was working on. The project was very challenging because of the lack of structural information and big amount of disordered regions. Still PyRy3D managed to propose interesting and satisfying solutions. So I can honestly recommend this software.