Bonvin LabJekyll2024-03-14T11:48:19+00:00https://www.bonvinlab.org/Alexandre Bonvinhttps://www.bonvinlab.org/a.m.j.j.bonvin@uu.nlhttps://www.bonvinlab.org/news/HADDOCK-ISGC2023-workshop2023-02-21T00:00:00+00:002023-02-21T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>We are organising a HADDOCK integrative modelling workshop at Academia Sinica in Taipei as a satellite event of the <a href="https://indico4.twgrid.org/event/25/">International Symposium on Grid and Cloud computing</a>. The workshop will take place on March 20th. Registration information can be found at the <a href="https://indico4.twgrid.org/event/25/page/46-registration">ISGC2023 website</a>.</p>
<p>This workshop (detailed programme <a href="https://indico4.twgrid.org/event/25/images/74-Workshop%20on%20Integrative%20modelling%20with%20HADDOCK_Final.jpg">here</a>) will consist of lectures and computer tutorials during which some of the recent HADDOCK developments will be discussed and demonstrated in hands-on computer tutorials. In particular we will introduce <a href="https://www.bonvinlab.org/software/haddock3/">HADDOCK3</a>, the new modular version of HADDOCK which represents a redesign of the HADDOCK2.X series, implementing new ways to interact with the HADDOCK sub-routines and offering more customization to the end user.</p>
<p><img src="/images/HADDOCK3-logo.png" alt="Structure + Binformatic/Biophysical Data => Complex" /></p>
<p>For the computer practical, participants are expected to bring their own laptop and register in advance to the <a href="https://nmrbox.nmrhub.org/events/events/2023-haddock-isgc-taipei">event</a> we created on <a href="https://nmrbox.nmrhub.org">NMRBOX</a> as we will be making use of those cloud resources for the HADDOCK3 workshop. Participants are encouraged to bring their own problems to get advice on the best modelling strategy.</p>
<p><a href="https://www.bonvinlab.org/news/HADDOCK-ISGC2023-workshop/">HADDOCK workshop at ISGC2023</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on February 21, 2023.</p>https://www.bonvinlab.org/news/HPC-innovation-award-for-deep-learning-work2020-12-15T00:00:00+00:002020-12-15T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>In the context of a <a href="https://www.surf.nl/en/the-surf-cooperative/surf-open-innovation-lab">SURF Open Innovation Lab</a> collaboration for <a href="https://www.surf.nl/en/exploring-machine-learning">deep learning enhanced HPC applications</a>, the consortium of several universities (WUR, Radboud, Utrecht and Leiden universities) and SURFSara, led by Caspar van Leeuwen and Axel Berg, have received for their work an <a href="https://www.hpcuserforum.com/innovationaward/winners.html">2020 HPC Innovation and ROI Award</a>.</p>
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<p>Part of the work involves our work on using deep learning to classify crystallographic interfaces as biological or crystal artifact. The approach builds on our <a href="https://www.esciencecenter.nl/projects/deeprank/">DeekRank project</a> in collaboration with the Netherlands <a href="https://www.esciencecenter.nl">e-Science Center</a>.</p>
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<p>Read the details in our whitepaper:</p>
<p>C. van Leeuwen, D. Podareanu, V. Codreanu, M. Cai, A. Berg, S. Portegies Zwart, R. Stoffer, M. Veerman, C. van Heerwaarden, S. Otten, S. Caron, C. Geng, F. Ambrosetti, A.M.J.J. Bonvin. <a href="https://www.surf.nl/files/2020-03/white-paper-dl4hpc-.pdf">Deep-learning enhancement of large scale numerical simulations</a>. Whitepaper (2020).</p>
<p><a href="https://www.bonvinlab.org/news/HPC-innovation-award-for-deep-learning-work/">HPC innovation award for deep learning work</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on December 15, 2020.</p>https://www.bonvinlab.org/news/Targeting-membrane-complexes2020-12-10T00:00:00+00:002020-12-10T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>Membrane proteins are among the most challenging systems to study with experimental techniques in the structural biology field. The increasing number of deposited structures of membrane proteins has opened the route to modeling their complexes by methods such as computational docking. We have developed a new protocol for the modeling of membrane-associated protein assemblies, which successfully integrates a simulated membrane calculated by the <a href="http://memprotmd.bioch.ox.ac.uk/">MemProtMD</a> database into a first docking step by <a href="https://lightdock.org">LightDock</a> with a flexible final refinement with <a href="https://haddock.science.uu.nl/haddock2.4/">HADDOCK</a>. This protocol should shed light on the still dark fraction of the interactome consisting of membrane proteins and will be extremely useful for drug discovery, antibody design and personalized medicine.</p>
<p><em>Nature Comm.</em> <em>11</em>, 6210 (2020)<br />
<a href="https://doi.org/10.1038/s41467-020-20076-5">https://doi.org/10.1038/s41467-020-20076-5</a></p>
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<p><a href="https://www.bonvinlab.org/news/Targeting-membrane-complexes/">Targeting membrane complexes</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on December 10, 2020.</p>https://www.bonvinlab.org/news/HADDOCK-EOSC-demo2020-05-28T00:00:00+00:002020-05-28T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>At the occasion of the <a href="https://www.eosc-hub.eu/events/eosc-hub-week-2020-goes-virtual">EOSC-Hub week conference</a> that took place online (May 18-20, 2020), Alexandre Bonvin gave during <a href="https://www.youtube.com/watch?v=IYj5DAIU19c&t=917">closing plenary session</a> an interview and live demo of the <a href="https://wenmr.science.uu.nl/haddock2.4">HADDOCK</a> thematic service. The demo shows how <a href="https://eosc-hub.eu">EOSC</a> enables the <a href="https://www.wenmr.eu">WeNMR</a> services to support thousands of researcher worldwide in the field of structural biology. WeNMR is linked to the <a href="https://instruct-eric.eu">Instruct-ERIC ESFRI</a>. The structural biology community has focused its efforts in the last months on providing answers to fight the Sarc-Cov-2 pandemic. The demo shows how the WeNMR services contribute to this research.</p>
<iframe width="560" height="315" src="https://www.youtube.com/embed/0uf-o4p1cH4" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe>
<p><a href="https://www.bonvinlab.org/news/HADDOCK-EOSC-demo/">Live demo of the HADDOCK EOSC portal</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on May 28, 2020.</p>https://www.bonvinlab.org/news/HADDDOCK-COVID-repurpusing2020-04-17T00:00:00+00:002020-04-17T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>The novel coronavirus (SARS-CoV-2) that has emerged from Wuhan, China in
December 2019 has spread to almost all countries in the World causing a
dramatic number of deaths. The current absence of antiviral treatment
against the SARS-CoV-2 urges the scientific community to accelerate the
drug discovery research process.</p>
<p>One way to identify potential treatments and to be able to administer it
swiftly is to focus on drug repurposing studies, i.e. to investigate the
SARS-CoV-2 antiviral potential of drugs that have already been approved
for human use.</p>
<p>Proteins that are crucial for the survival and replication of the virus
are the most attractive targets for such studies. We have focused on
the SARS-CoV-2 main protease (3CLpro) that plays an essential role in the
virus replication process by screening ~2000 approved drugs against this particular
protein. We used for that our HADDOCK software, powered by the HTC resources of <a href="https://eosc-hub.eu">EOSC</a>/<a href="https://www.egi.eu">EGI</a>.</p>
<p>More details and initial results are now available online <a href="/covid">here</a>.</p>
<p><a href="https://www.bonvinlab.org/news/HADDDOCK-COVID-repurpusing/">HADDDOCK COVID drug repurpusing</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on April 17, 2020.</p>https://www.bonvinlab.org/news/HTC-NWO-compute-grand-for-the-Utrecht-WeNMR-services2020-03-18T00:00:00+00:002020-03-18T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an integrative platform developed at Utrecht University for the modelling of biomolecular complexes. HADDOCK distinguishes itself from other docking methods in the fact that it can use a large variety of experimental and bioinformatics data to drive the docking process. HADDOCK can deal with a large class of modelling problems including protein-protein, protein-nucleic acids, protein-peptide and protein-ligand complexes.</p>
<p>Since 2008 HADDOCK has been offered as a web portal, freely accessible to non-profit users (wenmr.science.uu.nl) as part of the <a href="http://www.wenmr.eu">WeNMR</a> services. HADDOCK is also a thematic service in the <a href="https://marketplace.eosc-portal.eu">European Open Science Cloud marketplace</a>. This strategy has maximized the impact and valorisation of the research of <a href="http://www.bonvinlab.org">our group</a> (and the impact of NWO funding). Besides the application software, the service also provides automated pre- and post-processing, compute, temporary storage and job scheduling and monitoring for running the application, so that researchers do not need to worry about application porting and compute infrastructure. The portal is heavily used with >15500 registered users from >110 countries (<a href="https://wenmr.science.uu.nl/user_map">see statistics</a>), and receives a high number of citations.</p>
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<p><strong>We have obtained a NWO-ENW computing grant that allows us to maintain our services provisioning to serve the scientific community at large and maximise the impact of Dutch-funded research.</strong> Access to High Throughput Computing (HTC) grid resources is key. Not only does it allow to serve an international community, but it is also central to the research of the Utrecht group since significant computational recourses are required to keep developing new methods and model increasingly more complex and large macromolecular assemblies. The relevance of modelling biomolecular complexes is further highlighted by the fact that several major pharma companies are using our software. Our online services have also find their way into teaching as we see recurring registrations from students of various international universities.</p>
<p><a href="https://www.surf.nl/en/expertises/compute-services">SURFSara</a> and the Dutch Dutch National Grid Initiative have always supported the computing required by the Utrecht portals, providing resources for more than 70% of the jobs that run last year. This computing grant allows us to ensure the continued operation of our portals by renewing our access to the Dutch HTC grid resources. For this, we have been granted 8 million SBU wall clock hours (4M per year).</p>
<p><a href="https://www.bonvinlab.org/news/HTC-NWO-compute-grand-for-the-Utrecht-WeNMR-services/">High throughput computing NWO grant to support computational structural biology through the Utrecht WeNMR services</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on March 18, 2020.</p>https://www.bonvinlab.org/news/Fresh-doctor-Panos2020-03-09T00:00:00+00:002020-03-09T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>On February 26th, 2019, Panos Koukos successfully defended his PhD Thesis (read more below).</p>
<p>Another doctor in the group!</p>
<h3 id="well-done-and-congratulations">Well done and congratulations</h3>
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<p>Panos thesis entitled <em>Integrative modelling of biomolecular complexes: From small to large</em> focusses on biomolecular docking, a field of computational structural biology which concerns itself with solving 3D puzzles describing how biomolecules interact to form complexes. More specifically, it zooms into complexes involving proteins embedded in the membrane surrounding every cell, and complexes between small compounds and protein receptors of pharmaceutical interest.</p>
<p>The thesis begins by describing the current state of the art in integrative modelling approaches, with a particular emphasis on docking. Integrative modelling refers to computational methods that make use of diverse sources of data to guide the simulations. Chapters two and three are dealing with membrane protein complexes, first establishing a benchmark dataset and then describing a method to model those by docking. Chapters four to six are devoted to small molecule docking with the former two describing our successful participation in an international blind docking challenge, and the latter a novel method making use of shape information to guide the docking of small molecules into their receptors. The thesis ends with critical perspectives and areas of interest for future developments.</p>
<p><a href="https://www.bonvinlab.org/news/Fresh-doctor-Panos/">Panos Koukos successfully defends his PhD</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on March 09, 2020.</p>https://www.bonvinlab.org/news/Integrative-modelling-review2019-11-27T00:00:00+00:002019-11-27T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>Check out our fresh of the press review on <a href="https://doi.org/10.1016/j.jmb.2019.11.009" target="_blank"><em>Integrative Modelling of Biomolecular Complexes</em></a>.</p>
<p>It also discusses the modelling of membrane complexes.</p>
<p>Congratulations to Panos Koukos for a great job!</p>
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<p><a href="https://www.bonvinlab.org/news/Integrative-modelling-review/">Review on Integrative Modelling</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on November 27, 2019.</p>https://www.bonvinlab.org/news/2020EMBO-integrative-modelling-course2019-11-27T00:00:00+00:002019-11-27T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>Registration is open for the third edition of our EMBO practical course on Integrative Modelling of Biomolecular Complexes. It will take place Mayt 10-15, 2020 in Izmir, Turkey.</p>
<p>This course will present docking-based computational methods and related bioinformatics approaches, aiming at predicting how proteins interact with other biomolecules or ligands. Lectures will provide the theoretical background on state-of-the-art algorithms for sampling and scoring docking models, describe the use of low- and high-resolution information, and conservation- and coevolution-based interface prediction methods. Roughly half of the course wil consist of practical sessions where the students will run computations on interesting biological problems.</p>
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<p>Check the <a href="http://meetings.embo.org/event/20-biomolecular-interactions" target="_blank"><em>website</em></a> for the full programme and for registration information.</p>
<p>A poster can be downloaded <a href="/images/posts/20-biomolecular-interactions.pdf" target="_blank"><em>here</em></a></p>
<p><a href="https://www.bonvinlab.org/news/2020EMBO-integrative-modelling-course/">2020 EMBO integrative modelling course</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on November 27, 2019.</p>https://www.bonvinlab.org/news/Aye-Aye-Captain2019-05-01T00:00:00+00:002019-05-01T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>We have been since a long time contributing various software, including our HADDOCK flagship software, to <a href="https://sbgrid.org">SBGrid</a>. Read the recent story about a developer’s tale highlighting our research and HADDOCK.</p>
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<p><a href="https://sbgrid.org/software/tale/aye-aye-captain">https://sbgrid.org/software/tale/aye-aye-captain</a></p>
<p><a href="https://www.bonvinlab.org/news/Aye-Aye-Captain/">Aye Aye Captain</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on May 01, 2019.</p>https://www.bonvinlab.org/news/Coconuts-for-drug-design2019-04-30T00:00:00+00:002019-04-30T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>Our recent paper in the Journal of Chemical Information and Modelling introduces a computational approach based on metadynamics simulations called EDES – Ensemble-Docking with Enhanced-sampling of pocket Shape – that allows to generate holo-like conformations of proteins only exploiting their apo structures. This is achieved by defining a set of collective variables that effectively sample different shapes of the binding site, ultimately mimicking the steric effect due to ligands.</p>
<p>Our article features on the cover of JCIM with the analogy of a coconut showing a well open binding pocket compared to a filled watermelon not leaving any space for the ligand.</p>
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<p>We assessed the method on three challenging proteins undergoing different extents of conformational changes upon ligand binding. In all cases our protocol generates a significant fraction of structures featuring a low RMSD from the experimental holo geometry. Moreover, ensemble docking calculations using those conformations yielded in all cases native-like poses among the top ranked ones.</p>
<p>Read the full story at:</p>
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<li>A. Basciu, G. Malloci, F. Pietrucci, <strong>A.M.J.J. Bonvin</strong> and A.V. Vargiu.
<a href="http://dx.doi.org/10.1021/acs.jcim.8b00730">Holo-like and druggable protein conformations from enhanced-sampling of binding pocket shape</a>. <em>J. Chem. Inf. and Mod.</em> <em>59</em>, 1515–1528 (2019).</li>
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<p><a href="https://www.bonvinlab.org/news/Coconuts-for-drug-design/">Coconuts for drug design</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on April 30, 2019.</p>https://www.bonvinlab.org/news/Congratulations-to-Cunliang-for-his-PhD2019-02-27T00:00:00+00:002019-02-27T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>Last Monday (February 25th, 2019), Cunliang successfully defended his PhD.
Well done and congratulations!</p>
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<p>Want to know more about his PhD? Check his publications on <a href="https://scholar.google.nl/citations?hl=en&user=21G0R_AAAAAJ&view_op=list_works&sortby=pubdate">Google Scholar</a></p>
<p><a href="https://www.bonvinlab.org/news/Congratulations-to-Cunliang-for-his-PhD/">Congratulations to Cunliang for his PhD</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on February 27, 2019.</p>https://www.bonvinlab.org/news/HADDOCK-EGI-user-story2019-01-16T00:00:00+00:002019-01-16T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>Check out the recent research story published by <a href="http://www.egi.eu">EGI</a> showing how our HADDOCK portal making use of EGI and <a href="http://www.eosc-hub.eu">EOSC</a> resources is enabling scientists in their research.</p>
<p>Read the full story <a href="https://www.egi.eu/use-cases/research-stories/haddock-helps-scientists-to-look-at-the-evolution-of-brain-tumours/">here</a>.</p>
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<p><a href="https://www.bonvinlab.org/news/HADDOCK-EGI-user-story/">HADDOCK-EGI-user-story</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on January 16, 2019.</p>https://www.bonvinlab.org/news/Alexandre-Bonvin-about-EOSChub-in-practice2018-10-19T00:00:00+00:002018-10-19T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>The second edition of the <a href="https://eosc-hub.eu/news/eosc-hub-magazine-issue-2">EOSC-Hub</a> magazine features an interview with Alexandre Bonvin explaining how <a href="http://www.wenmr.eu">WeNMR</a> builds on EOSC-Hub resources to serve a worlwide community of researchers in structural biology and life sciences. WeNMR is operating as a <a href="https://eosc-hub.eu/catalogue/WeNMR%20suite%20for%20Structural%20Biology">thematic service provider</a> in EOSC-Hub.</p>
<p>The <a href="https://www.wenmr.eu/services/">WeNMR portals</a> cover different area of structural biology such as NMR structure calculations and data analysis (e.g. the AMBER, Xplor-NIH and FANTEN portals), the fitting of structural models into cryo-EM maps (PowerFit), the analysis of mass spectrometry cross-links (DisVis) or the integrative modelling of biomolecular complexes (HADDOCK). The tools are powered by High-Throughput Compute capabilities provided by the EGI Federation and enhanced with software components developed by the INDIGO DataCloud project.</p>
<p>In this interview, Alexandre Bonvin gives answer to the following questions:</p>
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<li>What are the main research goals of the WeNMR community?</li>
<li>How many people are involved in WeNMR?</li>
<li>What are the services that WeNMR provides, or wants to provide, to this collaboration?</li>
<li>What are the computational challenges?</li>
<li>The EOSC is being set up to be Europe’s virtual environment for all researchers to store, manage, analyse and re-use data for research, innovation and educational purposes. How will you interact with this environment?</li>
<li>How do you imagine your field in ten years?</li>
</ul>
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<p>EOSC-hub is an European Union’s Horizon 2020 project that brings together multiple service providers to create the Hub: a single contact point for European researchers and innovators to discover, access, use and reuse a broad spectrum of resources for advanced data-driven research. For researchers, this means a broader access to services supporting their scientific discovery and collaboration across disciplinary and geographical boundaries.</p>
<p><a href="https://www.bonvinlab.org/news/Alexandre-Bonvin-about-EOSChub-in-practice/">Alexandre Bonvin about EOSChub in practice</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on October 19, 2018.</p>https://www.bonvinlab.org/news/Top-performance-of-the-HADDOCK-team-in-D3R2018-08-21T00:00:00+00:002018-08-21T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>In a recent article we report the performance of HADDOCK in the 2018 iteration of the Grand Challenge organised by the <a href="https://drugdesigndata.org">D3R</a> consortium. Building on the <a href="https://doi.org/10.1007/s10822-017-0049-y">findings of our participation in last year’s challenge</a>, we significantly improved our pose prediction protocol which resulted in a mean RMSD for the top scoring pose of 3.04 and 2.67 Å for the cross-docking and self-docking experiments respectively, which corresponds to an overall success rate of 63% and 71% when considering the top1 and top5 models respectively.</p>
<p>This performance ranks HADDOCK as the 6th and 3rd best performing group (excluding multiple submissions from a same group) out of a total of 44 and 47 submissions respectively.</p>
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<i>Superpositions of HADDOCK models on reference structures.<br />Left: model 5 from target 1 (1.1Å). Right: model 1 from target 8 (1.5Å).</i></p>
<p>Our ligand-based binding affinity predictor is the 3rd best predictor overall, behind only the two leading structure-based implementations, and the best ligand-based one with a Kendall’s Tau correlation of 0.36 for the Cathepsin challenge. It also performed well in the classification part of the Kinase challenges, with Matthews Correlation Coefficients of 0.49 (ranked 1st), 0.39 (ranked 4th) and 0.21 (ranked 4th) for the JAK2, vEGFR2 and p38a targets respectively.</p>
<p>Through our participation in last year’s competition we came to the conclusion that <em>template selection is of critical importance for the successful outcome of the docking</em>. This year we have made improvements in two additional areas of importance: <em>ligand conformer selection</em> and <em>initial positioning</em>, which have been key to our excellent pose prediction performance this year.</p>
<p>The data and code used to train the ligand-based binding affinity predictor and rank the compounds are freely available on GitHub, together with our in-house scripts developed during our participation in the last two GC competitions. These can be accessed at following URL: <a href="https://github.com/haddocking/D3R-tools">https://github.com/haddocking/D3R-tools</a>.</p>
<p>Read all details in our publication:</p>
<ul>
<li>P.I. Koukos, L.C. Xue and <strong>A.M.J.J. Bonvin</strong>. <a href="https://doi.org/10.1007/s10822-018-0148-4">Protein-ligand pose and affinity prediction. Lessons from D3R Grand Challenge 3</a>. <em>J. Comp. Aid. Mol. Des.</em> Advanced Online Publication (2018).</li>
</ul>
<p><a href="https://www.bonvinlab.org/news/Top-performance-of-the-HADDOCK-team-in-D3R/">Top performance of the HADDOCK team in D3R Grand Challenge 3</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on August 21, 2018.</p>https://www.bonvinlab.org/news/Over-200000-served-HADDOCK-runs2018-06-27T00:00:00+00:002018-06-27T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>Our <a href="https://haddock.science.uu.nl">HADDOCK web portal</a> passed today the cap of over 200’000 served docking runs since June 2008. 40% of those have run on <a href="http://www.egi.eu">EGI</a> / <a href="http://www.eosc-hub.eu">EOSC-Hub</a> e-Infrastructure HTC resources, not to forget the strong support from the Dutch e-Infrastructure resources from <a href="http://www.surfsara.nl">SURFSara</a> and <a href="http://www.nikhef.nl">Nihkef</a> where about 70% of our jobs are running.</p>
<p>HADDOCK is one of the flagship software in the H2020 EU Center of Excellence project <a href="http://www.bioexcel.eu">BioExcel</a>.</p>
<figure>
<img align="center" src="/images/posts/HADDOCK-stats-06-2018.png" />
</figure>
<p>Our HADDOCK portal now counts over 11’000 registered users from over 95 different countries worldwide.</p>
<figure>
<a href="https://bianca.science.uu.nl/user_map"><img align="center" src="/images/posts/HADDOCK-worldmap-06-2018.png" /></a>
</figure>
<p><a href="https://www.bonvinlab.org/news/Over-200000-served-HADDOCK-runs/">Over 200000 served HADDOCK runs</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on June 27, 2018.</p>https://www.bonvinlab.org/news/New-HADDOCK-server-coming-up2018-05-25T00:00:00+00:002018-05-25T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>In the context of the <a href="https://about.west-life.eu">WestLife</a> and <a href="http://www.bioexcel.eu">BioExcel</a> EU projects we have been working hard on a complete new design (and machinery) of our HADDOCK portal. The new version (HADDOCK2.4) does support cryo-EM data and will allow multibody docking up to 20 molecules.</p>
<p>We just published as a WestLife project deliverable a description of its implementation available in Zenodo (DOI:<a href="https://doi.org/10.5281/zenodo.1252960">10.5281/zenodo.1252961</a>).</p>
<p>We will soon be looking for beta testers to get feedback before putting it in production mode.
So if you are interested, do contact us at <em>software.csb_at_bonvinlab.org</em>.</p>
<p><a href="https://www.bonvinlab.org/news/New-HADDOCK-server-coming-up/">New HADDOCK2.4 server coming up</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on May 25, 2018.</p>https://www.bonvinlab.org/news/BioExcel-summerschool2018-02-20T00:00:00+00:002018-02-20T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>The BioExcel summerschool on biomolecular simulations will take place in June on the beautiful island of Sardinia.
The course will start on Monday June 18th (arrival on Sunday) and last until Friday morning.
The cost of the school, which includes meals, accomodation and local transport is 265.- UK pounds.</p>
<p>For registration (which closes on March 30) see:</p>
<p><a href="https://bioexcel.eu/events/summerschool-2018">https://bioexcel.eu/events/summerschool-2018</a></p>
<figure>
<img align="center" src="/images/posts/BioExcel-summerschool.png" />
</figure>
<p><a href="https://www.bonvinlab.org/news/BioExcel-summerschool/">BioExcel Summerschool</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on February 20, 2018.</p>https://www.bonvinlab.org/news/HADDOCK-10K-users2017-11-13T00:00:00+00:002017-11-13T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>Our <a href="http://haddock.science.uu.nl/services/HADDOCK2.2">HADDOCK web portal</a> has reached today a new milestone with 10000 registered users from all around the world!</p>
<figure>
<img align="center" src="/images/posts/HADDOCK-10K.png" />
</figure>
<p>Since June 2008, the server has processed over 180’000 docking runs, about 35% of whose have run on the High Throughput Computing (HTC) resources of <a href="href="http://www.egi.eu">EGI</a> building on the European e-Infrastructure. The continuous development and operation of the HADDOCK web portal has been made possible over the years thanks to the support of <a href="http://www.uu.nl">Utrecht University</a>, the <a href="http://bijvoet-center.eu">Bijvoet Center for Biomolecular Research</a> and various grant agencies and projects.</p>
<center>
<a href="http://www.uu.nl"><img src="/images/UU_logo-small.png" /></a>
<p>
<a href="http://www.nwo.nl"><img src="/images/NWO_logo-small.png" /></a>
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<a href="http://www.egi.eu"><img height="70" src="/images/EGI_logo-small.png" /></a>
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<a href="http://www.wenmr.eu"><img src="/images/WeNMR_logo-small.png" /></a>
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<a href="http://www.west-life.eu"><img src="/images/West-Life_logo-small.png" /></a>
<p>
<a href="http://www.indigo-datacloud.eu"><img src="/images/INDIGO_logo-small.png" /></a>
<p>
<a href="http://www.bioexcel.eu"><img src="/images/Bioexcel_logo-small.png" /></a>
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<a href="http://ec.europa.eu/programmes/horizon2020/en/h2020-section/research-infrastructures-including-e-infrastructures"><img height="30" src="/images/H2020_logo-small.png" /></a>
</center>
</p></p></p></p></p></p></p></center>
<p><a href="https://www.bonvinlab.org/news/HADDOCK-10K-users/">HADDOCK reaches 10K users</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on November 13, 2017.</p>https://www.bonvinlab.org/news/HADDOCK-expands-to-support-20-molecules2017-10-20T00:00:00+00:002017-10-20T00:00:00+00:00Alexandre Bonvinhttps://www.bonvinlab.orga.m.j.j.bonvin@uu.nl<p>With our recent <a href="https://doi.org/10.1038/nmeth.4392">Nature Methods</a> publication we have now officially extended HADDOCK to support up to 20 separate molecules, expanding its capabilities as truly integrative modelling platform.</p>
<figure align="center">
<img src="/images/posts/HADDOCK-M3-example.png" />
</figure>
<center>
<i>Example of a complex protein structure calculated with the new HADDOCK framework:<br />
the box C/D enzyme for RNA methylation.</i>
</center>
<p><br />
To deal with such a larger number of molecules, the initial random positioning of the components and the minimisation stage have been optimised. The paper also describes a method to select the most likely models after rigid-body docking and up-sample them during flexible refinement.</p>
<p>We hope in a near future to release a new version of our <a href="haddock.science.uu.nl">HADDOCK web portal</a> that will support this new version, together with cryo-EM restraints among others. In the mean time this new HADDOCK version can be obtained for local installation upon request (the official distribution remains version2.2 at this time).</p>
<p>Read more about this in our publication:</p>
<ul>
<li>E. Karaca, J.P.G.L.M. Rodrigues, A. Graziadei, <strong>A.M.J.J. Bonvin</strong> and T. Carlomagno. <a href="https://doi.org/10.1038/nmeth.4392">An Integrative Framework for Structure Determination of Molecular Machines</a>. <em>Nature Methods</em> <em>14</em>, 897-902 (2017).</li>
</ul>
<p>And in the following <a href="https://www.uu.nl/en/news/new-platform-for-elucidation-of-large-protein-and-nucleic-acid-structures-in-infections"><strong>news item</strong></a>.</p>
<p><a href="https://www.bonvinlab.org/news/HADDOCK-expands-to-support-20-molecules/">HADDOCK expands to support 20 molecules</a> was originally published by Alexandre Bonvin at <a href="https://www.bonvinlab.org">Bonvin Lab</a> on October 20, 2017.</p>