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SMLMC15
Structural Modelling for Large Macromolecular ComplexesSome Testimonialsfrom users that attended a similar course in 2014 |
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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 PompeiaUniv. Estadual Paulista, Brazil The course (in Oeiras, Portugal, lead by the developerof PyRy3D 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. Michal Taube PhD student, Adam Mickiewicz University in Poznan, Poland 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 Ciência, Oeiras, Portugal 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. |
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Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: Mar 12th 2015 |