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Welcome!
Winter is on its way, days are getting shorter and there is nothing better than another issue of your favorite newsletter to cheer you up! Please spread the word and forward it to your friends and colleagues.
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This month, we have a terrific program to share with you! As usual, we selected two must-read papers that have just been released, both introducing integrative modelling platforms and new features. We also share with you the nice interview of Maya Topf, who contributed to the development of many computational methods and software in the field of 3D-EM data integration and model analysis. In case you missed it last month, here is another chance to read the very nice review published by her group last summer. And the cherry on the cake, another edition of the eagerly awaited tips and tricks!
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We also would like to invite you to register asap for our face-to-face BioExcel Community Forum that will take place in Amsterdam on the 22nd and 23rd of November. Registration is free for all the members of an interest group and we encourage you to book your stay at the venue, which is the Lloyd Hotel. Further details and the link for registration is on the BioExcel web site.
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Don't miss this opportunity to meet the developers of the main software supported by BioExcel (GROMACS, HADDOCK and CPMD) and to engage with your peers in a unique, community-driven scientific event. This two days forum is a networking event with a programme of parallel interactive sessions, each organized by the interest groups leaders, with the possibility for all attendees to move between. Spoiler alert: we are busy preparing the first hands-on session that will combine both integrative modelling and hybrid methods interest groups! It will also feature our new collaborators from VU Amsterdam who develop MDstudio (see the webinar here) and other guests for intense discussions along the event. Check the program and the venue can be found here.
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We hope to trigger some discussions on the interest group and really encourage you to contribute to the upcoming issues of our newsletter by suggesting events/articles on the IG-IM forum.
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As usual, a digest of all those posts can be found on the main page of our community.
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Lights on... Maya Topf - creator of TEMPy
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Prof. Dr. Maya Topf got her PhD degree at the University of Oxford in 2002 where she used hybrid QM/MM and classical molecular dynamics simulations to study serine protease deacetylation. She then moved to the University of San Francisco to join Andrej Sali's lab (don't miss their last paper on IMP also highlighted in this newsletter!) where she successfully combined cryo-electron microscopy data and comparative modelling to model macromolecular structures at an atomic resolution.
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Later on, Maya came back to UK at the Institute of Structural and Molecular Biology and Birkbeck, where she could further work at the interface between bioinformatics and cryo-electron microscopy. Over the last years, the Topf group developed numerous methods to integrate experimental data into the modelling process of macromolecular assemblies, focusing on 3D-EM and mass spectrometry data. Among them, they released TEMPy, a python library to assess the fits of atomic models in 3D electro-microscopy density maps ...
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Publications
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Protein Sci.
SUMMARY: Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function... Read more
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Nature Methods, 14(9):897-902.
SUMMARY: We present a broadly applicable, user-friendly protocol that incorporates sparse and hybrid experimental data to calculate quasi-atomic-resolution structures of molecular machines. The protocol uses the HADDOCK framework, accounts for extensive structural rearrangements both at the domain and atomic levels and accepts input from all structural and biochemical experiments whose data can be translated into interatomic distances and/or molecular shapes. Read more
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Upcoming events
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Tips & Tricks
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Neither a secret trick nor an esoteric package this week but let's highlight a great resource both for biomolecular scientists and computational biologists: OMICtools. OMICtools is a manually curated database of biological data analysis tools. It provides an overview of more than 22,000 software and databases with a particular focus on omics data, specifying the supported operating systems and listing the different interfaces. Adepts of web portals or developers willing to extend their analysis pipelines, web servers and APIs are listed there waiting for you to create tomorrow's workflows for life sciences.
Read more about it here!
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