Deliverables Documents, reports (26) Development of a framework for the combination of HPC and HPDA operations Report on the design and development of initial workflows combining HPC and HPDA operations Best Practice Guides A collection of best practices developed for the core project codes and related work in T34 Quality assurance and risk management plan This deliverable will discuss the overall quality monitoring process for the project (such as deliverables and milestone completion, KPIs) and the overall risk management strategy. The risks will be regularly assessed in the mandatory management reports. Updated specification of development process A report specifying the software engineering testing and quality assurance aspects of the project building on past efforts and adapting them to new codes and changed contexts This will also include a report of the BioExcel CP2K profiling outcome Business Model design report Detailed BioExcel Business Model for taking the project into a sustainability phase Provision of a Workflow Environment at BioExcel portal Report on the updates implemented in the BioExcel Cloud Portal Integration of BioExcel software framework with standards and international initiatives The deliverable will detail the integration of BioExcel computational framework with external initiatives like ELIXIR GA4GH Update of whitepaper on scientific software development Publication of an updated version of the scientific software development white paper published by the first BioExcel project This should reflect the current state of software development of the BioExcel codes as well updates to reflect changes in software development standards Exascale co-design benchmark cases Key kernels from the core applications will be extracted to become useful to vendor or tool implementers as optimization targets Updated software roadmaps The roadmap for each of the core applications will be updated for new changes to HPC hardware and software contexts user requests and progress since previous roadmaps Work Plans for UCs This deliverable will contain the detailed workplans for the use cases Branding and Quality Mark Design Inception Report An initial document setting the vision for the CoE brand as a European Centre promoting quality Pre-Exascale showcase calculation and Use Case Final Report A large preExascale showcase calculation will be performed and analysed This deliverable will also include a final report on the work undertaken on the projects use cases User Community Support and Engagement Report (final) An update to D34 to include work from the second half of the project in the same areas as D34 along with a summary of feedback from the CAPRI workshop or relevant T36 work Annotated and justified Service Catalogue A first list of exploitable assets identified Management Plan Initial deliverable stating the management organization and planning for the entire project Dissemination and outreach plan This document will outline the overall plan for dissemination and outreach activities of the CoE State-of-the-art and Initial Roadmap This deliverable will summarise and describe the new technologies, methods and tools identified and collected to be used in the project workflows. From these, an initial roadmap will be proposed. User Community Support and Engagement Report (half-time update) Reports from events community support engagement activities and summary of feedback provided to the rest of the project This report will also include results and analysis of the first and second user surveys Final report on dissemination and training Report on the status and outcome of the disseminationoutreach activities and the training programme during the second half of the project Long-term hardware and application roadmap The roadmap for each of the core applications will be related to what has been achieved in BioExcel2 and updated for new changes to HPC hardware and software contexts user requests and progress since previous roadmaps An update to D13 High Performance Computing in support of COVID-19 Research Description of BioExcels work in the global efforts against Covid19 Use Case Progress Report An update on the progress of the use cases Progress report and update on training and dissemination plan This document will report on the status and outcome of the dissemination/outreach activities and the training programme. Additionally, it will present updated plans for the second half of the project. First release of workflow-ready building blocks library This deliverable will describe the design and development of the first release of the building blocks library. Training Plan This document will include a report of the updated competency profile, an evaluation of the virtual training pilots, and outline of the BioExcel Training programme. Other (2) First release of demonstration workflows This deliverable will cover the first release of demonstration workflows. It will include an update of the initial roadmap. Project release of core applications Public release of all current code development within the project, with accompanying documentation, tests, benchmarks, and benchmark reports. Open Research Data Pilot (1) Data Management Plan The data management plan for the use cases Publications Peer reviewed articles (62) The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry Author(s): Montserrat Terrazas, Vito Genna, Guillem Portella, Núria Villegas, Dani Sánchez, Carme Arnan, Carlos Pulido-Quetglas, Rory Johnson, Roderic Guigó, Isabelle Brun-Heath, Anna Aviñó, Ramon Eritja, Modesto Orozco Published in: Chem, Issue 5/6, 2019, Page(s) 1619-1631, ISSN 2451-9294 Publisher: Elsevier DOI: 10.1016/j.chempr.2019.04.002 A molecular mechanism for transthyretin amyloidogenesis Author(s): Ai Woon Yee, Matteo Aldeghi, Matthew P. Blakeley, Andreas Ostermann, Philippe J. Mas, Martine Moulin, Daniele de Sanctis, Matthew W. Bowler, Christoph Mueller-Dieckmann, Edward P. Mitchell, Michael Haertlein, Bert L. de Groot, Elisabetta Boeri Erba, V. Trevor Forsyth Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-019-08609-z Computational approaches to therapeutic antibody design: established methods and emerging trends Author(s): Richard A Norman, Francesco Ambrosetti, Alexandre M J J Bonvin, Lucy J Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk Published in: Briefings in Bioinformatics, 2019, ISSN 1467-5463 Publisher: Oxford University Press DOI: 10.1093/bib/bbz095 LightDock goes information-driven Author(s): Jorge Roel-Touris, Alexandre M J J Bonvin, Brian Jiménez-García Published in: Bioinformatics, Issue 36/3, 2019, Page(s) 950-952, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btz642 Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3 Author(s): Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin Published in: Journal of Computer-Aided Molecular Design, Issue 33/1, 2019, Page(s) 83-91, ISSN 0920-654X Publisher: Kluwer Academic Publishers DOI: 10.1007/s10822-018-0148-4 An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45 Author(s): Panagiotis I. Koukos, Jorge Roel‐Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E. Trellet, Adrien S. J. Melquiond, Li C. Xue, Rodrigo V. Honorato, Irina Moreira, Zeynep Kurkcuoglu, Anna Vangone, Alexandre M. J. J. Bonvin Published in: Proteins: Structure, Function, and Bioinformatics, Issue 88/8, 2020, Page(s) 1029-1036, ISSN 0887-3585 Publisher: Wiley-Liss Inc DOI: 10.1002/prot.25869 Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond Author(s): Alexandra Balaceanu, Diana Buitrago, Jürgen Walther, Adam Hospital, Pablo D Dans, Modesto Orozco Published in: Nucleic Acids Research, Issue 47/9, 2019, Page(s) 4418-4430, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkz255 Molywood: streamlining the design and rendering of molecular movies Author(s): Miłosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco Published in: Bioinformatics, 2020, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btaa584 Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures Author(s): H.M. Berman, P,D. Adams, A.M.J.J. Bonvin, S.K. Burley, B. Carragher, W. Chiu, F. DiMaio, T.E. Ferrin, M.J. Gabanyi, T.D. Goddard, P.R. Griffin, J. Haas, C.A. Hanke, J.C. Hoch, G. Hummer, G. Kurisu, C.L. Lawson, A. Leitner, J.L. Markley, J. Meiler, G.T. Montelione, G.N. Phillips Jr., T. Prisner, J. Rappsilber, D.C. Schriemer, T. Schwede, C.A.M. Seidel, T.S. Strutzenberg, D.I. Svergun, E. Tajkhorshi Published in: Structure, Issue 27/12, 2019, Page(s) 1745-1759, ISSN 2352-0124 Publisher: Elsevier Limited DOI: 10.1016/j.str.2019.11.002 An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations Author(s): Antonija Kuzmanic, Pablo D. Dans, Modesto Orozco Published in: Chem, Issue 5/3, 2019, Page(s) 649-663, ISSN 2451-9294 Publisher: Elsevier DOI: 10.1016/j.chempr.2018.12.007 A multifunctional toolkit for target-directed cancer therapy Author(s): Montserrat Terrazas, Dani Sánchez, Federica Battistini, Núria Villegas, Isabelle Brun-Heath, Modesto Orozco Published in: Chemical Communications, Issue 55/6, 2019, Page(s) 802-805, ISSN 1359-7345 Publisher: Royal Society of Chemistry DOI: 10.1039/c8cc08823c iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations Author(s): Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin Published in: Proteins: Structure, Function, and Bioinformatics, Issue 87/2, 2019, Page(s) 110-119, ISSN 0887-3585 Publisher: Wiley-Liss Inc DOI: 10.1002/prot.25630 Natural helix 9 mutants of PPARγ differently affect its transcriptional activity Author(s): Marjoleine F. Broekema, Maarten P.G. Massink, Cinzia Donato, Joep de Ligt, Joerg Schaarschmidt, Anouska Borgman, Marieke G. Schooneman, Diana Melchers, Martin N. Gerding, René Houtman, Alexandre M.J.J. Bonvin, Amit R. Majithia, Houshang Monajemi, Gijs W. van Haaften, Maarten R. Soeters, Eric Kalkhoven Published in: Molecular Metabolism, Issue 20, 2019, Page(s) 115-127, ISSN 2212-8778 Publisher: Elsevier GmbH DOI: 10.1016/j.molmet.2018.12.005 DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region Author(s): Anna Cuppari, Pablo Fernández-Millán, Federica Battistini, Aleix Tarrés-Solé, Sébastien Lyonnais, Guillermo Iruela, Elena Ruiz-López, Yuliana Enciso, Anna Rubio-Cosials, Rafel Prohens, Miquel Pons, Carlos Alfonso, Katalin Tóth, Germán Rivas, Modesto Orozco, Maria Solà Published in: Nucleic Acids Research, Issue 47/12, 2019, Page(s) 6519-6537, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkz406 Modeling, Simulations, and Bioinformatics at the Service of RNA Structure Author(s): Pablo D. Dans, Diego Gallego, Alexandra Balaceanu, Leonardo Darré, Hansel Gómez, Modesto Orozco Published in: Chem, Issue 5/1, 2019, Page(s) 51-73, ISSN 2451-9294 Publisher: Elsevier DOI: 10.1016/j.chempr.2018.09.015 Integrative Modelling of Biomolecular Complexes Author(s): P.I. Koukos, A.M.J.J. Bonvin Published in: Journal of Molecular Biology, Issue 432/9, 2020, Page(s) 2861-2881, ISSN 0022-2836 Publisher: Academic Press DOI: 10.1016/j.jmb.2019.11.009 Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase Author(s): Leander Goldbach, Bram J. A. Vermeulen, Sami Caner, Minglong Liu, Christina Tysoe, Lieke van Gijzel, Ryoji Yoshisada, Mikael Trellet, Hugo van Ingen, Gary D. Brayer, Alexandre M. J. J. Bonvin, Seino A. K. Jongkees Published in: ACS Chemical Biology, Issue 14/8, 2019, Page(s) 1751-1759, ISSN 1554-8929 Publisher: American Chemical Society DOI: 10.1021/acschembio.9b00290 Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype–phenotype correlation Author(s): Emanuele G. Coci, Vytautas Gapsys, Natasha Shur, Yoon Shin‐Podskarbi, Bert L. Groot, Kathryn Miller, Jerry Vockley, Neal Sondheimer, Rebecca Ganetzky, Peter Freisinger Published in: Human Mutation, Issue 40/6, 2019, Page(s) 816-827, ISSN 1059-7794 Publisher: John Wiley & Sons Inc. DOI: 10.1002/humu.23742 Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC Author(s): Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher, Emiliano Ippoliti, Paolo Carloni, Ursula Rothlisberger Published in: Journal of Chemical Theory and Computation, Issue 15/10, 2019, Page(s) 5601-5613, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.9b00424 A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) Author(s): Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, Alexandre M.J.J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock, Manuela Helmer-Citterich, Adam Hospital, Modesto Orozco, Anastassis Perrakis, Matthias Rarey, Claudio Soares, Joel L. Sussman, Janet M. Thornton, Pierre Tuffery, Gabor Tusnady, Rikkert Wierenga, Tiina Salminen, Bohdan S Published in: F1000Research, Issue 9, 2020, Page(s) 278, ISSN 2046-1402 Publisher: F1000 Research Ltd. DOI: 10.12688/f1000research.20559.1 Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches Author(s): Matteo Aldeghi, Vytautas Gapsys, Bert L. de Groot Published in: ACS Central Science, Issue 5/8, 2019, Page(s) 1468-1474, ISSN 2374-7943 Publisher: ACS Central Science DOI: 10.1021/acscentsci.9b00590 How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition Author(s): Federica Battistini, Adam Hospital, Diana Buitrago, Diego Gallego, Pablo D. Dans, Josep Lluis Gelpí, Modesto Orozco Published in: Journal of Molecular Biology, Issue 431/19, 2019, Page(s) 3845-3859, ISSN 0022-2836 Publisher: Academic Press DOI: 10.1016/j.jmb.2019.07.021 Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering. Author(s): Marie Lycksell; Urska Rovsnik; Cathrine Bergh; Nicolai Tidemand Johansen; Anne L. Martel; Lionel Porcar; Lise Arleth; Rebecca J. Howard; Erik Lindahl; Erik Lindahl Published in: 'Proceedings of the National Academy of Sciences ', vol: 118 , pages: e2108006118-1-e2108006118-9 (2021), Issue 75, 2021, ISSN 0027-8424 Publisher: National Academy of Sciences DOI: 10.1073/pnas.2108006118 The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser Author(s): Elin Claesson, Weixiao Yuan Wahlgren, Heikki Takala, Suraj Pandey, Leticia Castillon, Valentyna Kuznetsova, Léocadie Henry, Matthijs Panman, Melissa Carrillo, Joachim Kübel, Rahul Nanekar, Linnéa Isaksson, Amke Nimmrich, Andrea Cellini, Dmitry Morozov, Michał Maj, Moona Kurttila, Robert Bosman, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, So Iwata, Shigeki Owada, Keith Moffat, Gerrit Published in: eLife, Issue 9, 2020, ISSN 2050-084X Publisher: eLife Sciences Publications DOI: 10.7554/elife.53514 Pre-exascale computing of protein-ligand binding free energies with open source software for drug design. Author(s): Vytautas Gapsys; David F. Hahn; Gary Tresadern; David L. Mobley; Markus Rampp; Bert L. de Groot Published in: Journal of Chemical Information and Modeling, Issue 62, 2021, ISSN 1549-9596 Publisher: American Chemical Society DOI: 10.1021/acs.jcim.1c01445 Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4 Author(s): Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu Published in: Journal of Computer-Aided Molecular Design, Issue 34/2, 2020, Page(s) 149-162, ISSN 0920-654X Publisher: Kluwer Academic Publishers DOI: 10.1007/s10822-019-00244-6 The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules Author(s): Pablo D Dans, Alexandra Balaceanu, Marco Pasi, Alessandro S Patelli, Daiva Petkevičiūtė, Jürgen Walther, Adam Hospital, Genís Bayarri, Richard Lavery, John H Maddocks, Modesto Orozco Published in: Nucleic Acids Research, Issue 47/21, 2019, Page(s) 11090-11102, ISSN 0305-1048 Publisher: Oxford University Press DOI: 10.1093/nar/gkz905 Surviving the deluge of biosimulation data Author(s): Adam Hospital, Federica Battistini, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco Published in: WIREs Computational Molecular Science, Issue 10/3, 2020, ISSN 1759-0876 Publisher: John Wiley & Sons Inc. DOI: 10.1002/wcms.1449 Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment Author(s): Marc F. Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil, Tereza Gerguri, Paul A. Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran‐Ran Liu, Xi‐Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov, Published in: Proteins: Structure, Function, and Bioinformatics, Issue 87/12, 2019, Page(s) 1200-1221, ISSN 0887-3585 Publisher: Wiley-Liss Inc DOI: 10.1002/prot.25838 Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset Author(s): Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga Published in: Journal of Computer-Aided Molecular Design, Issue 33/12, 2019, Page(s) 1031-1043, ISSN 0920-654X Publisher: Kluwer Academic Publishers DOI: 10.1007/s10822-019-00232-w Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked Author(s): Satu Mustalahti, Dmitry Morozov, Hoi Ling Luk, Rajanish R. Pallerla, Pasi Myllyperkiö, Mika Pettersson, Petri M. Pihko, Gerrit Groenhof Published in: The Journal of Physical Chemistry Letters, Issue 11/6, 2020, Page(s) 2177-2181, ISSN 1948-7185 Publisher: American Chemical Society DOI: 10.1021/acs.jpclett.0c00060 Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape Author(s): Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu Published in: Journal of Chemical Information and Modeling, Issue 59/4, 2019, Page(s) 1515-1528, ISSN 1549-9596 Publisher: American Chemical Society DOI: 10.1021/acs.jcim.8b00730 Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling Author(s): Multamäki, Elina; Nanekar, Rahul; Morozov, Dmitry; Lievonen, Topias; Golonka, David; Wahlgren, Weixiao Yuan; Stucki-Buchli, Brigitte; Rossi, Jari; Hytönen, Vesa P.; Westenhoff, Sebastian; Ihalainen, Janne A.; Möglich, Andreas; Takala, Heikki Published in: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021), Issue 45, 2021, ISSN 2041-1723 Publisher: Nature Publishing Group Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development Author(s): O.M.H. Salo-Ahen, I. Alanko, R. Bhadane, A.M.J.J. Bonvin, R. Vargas Honorato, S. Hossain, A.H. Juffer, A. Kabedev, M. Lahtela-Kakkonen, A. Støttrup Larsen, E. Lescrinier, P. Marimuthu, M. Mirza, G. Mustafa, A. Nunes-Alves, T. Pantsar, A. Saadabadi, K. Singaravelu, M. Vanmeert. Published in: Processes, Issue 9(1), 2021, Page(s) 71, ISSN 2227-9717 Publisher: MDPI DOI: 10.3390/pr9010071 Mode of action of teixobactins in cellular membranes Author(s): Rhythm Shukla, João Medeiros-Silva, Anish Parmar, Bram J. A. Vermeulen, Sanjit Das, Alessandra Lucini Paioni, Shehrazade Jekhmane, Joseph Lorent, Alexandre M. J. J. Bonvin, Marc Baldus, Moreno Lelli, Edwin J. A. Veldhuizen, Eefjan Breukink, Ishwar Singh, Markus Weingarth Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-020-16600-2 EXPLORING THE CONFORMATIONAL LANDSCAPE OF BIOACTIVE SMALL MOLECULES Author(s): Sanja Zivanovic, Francesco Colizzi, David Moreno, Adam Hospital, Robert Soliva, Modesto Orozco Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.0c00304 Finding the ΔΔ G spot: Are predictors of binding affinity changes upon mutations in protein-protein interactions ready for it? Author(s): Cunliang Geng, Li C. Xue, Jorge Roel-Touris, Alexandre M. J. J. Bonvin Published in: Wiley Interdisciplinary Reviews: Computational Molecular Science, Issue 9/5, 2019, Page(s) e1410, ISSN 1759-0876 Publisher: John Wiley & Sons Inc. DOI: 10.1002/wcms.1410 An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases Author(s): Juan Aranda, Montserrat Terrazas, Hansel Gómez, Núria Villegas, Modesto Orozco Published in: Nature Catalysis, Issue 2/6, 2019, Page(s) 544-552, ISSN 2520-1158 Publisher: Nature DOI: 10.1038/s41929-019-0290-y The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations Author(s): Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera Published in: Journal of Computer-Aided Molecular Design, Issue 34/5, 2020, Page(s) 601-633, ISSN 0920-654X Publisher: Kluwer Academic Publishers DOI: 10.1007/s10822-020-00290-5 Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK Author(s): Jorge Roel-Touris, Charleen G. Don, Rodrigo V. Honorato, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin Published in: Journal of Chemical Theory and Computation, Issue 15/11, 2019, Page(s) 6358-6367, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.9b00310 Molecular Basis of CLC Antiporter Inhibition by Fluoride Author(s): Maria Gabriella Chiariello, Viacheslav Bolnykh, Emiliano Ippoliti, Simone Meloni, Jógvan Magnus Haugaard Olsen, Thomas Beck, Ursula Rothlisberger, Christoph Fahlke, Paolo Carloni Published in: Journal of the American Chemical Society, Issue 142/16, 2020, Page(s) 7254-7258, ISSN 0002-7863 Publisher: American Chemical Society DOI: 10.1021/jacs.9b13588 Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor Author(s): Albert Escobedo, Busra Topal, Micha B. A. Kunze, Juan Aranda, Giulio Chiesa, Daniele Mungianu, Ganeko Bernardo-Seisdedos, Bahareh Eftekharzadeh, Margarida Gairí, Roberta Pierattelli, Isabella C. Felli, Tammo Diercks, Oscar Millet, Jesús García, Modesto Orozco, Ramon Crehuet, Kresten Lindorff-Larsen, Xavier Salvatella Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723 Publisher: Nature Publishing Group DOI: 10.1038/s41467-019-09923-2 Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design Author(s): Yuriy Khalak; Gary Tresadern; Matteo Aldeghi; Hannah Magdalena Baumann; David L. Mobley; Bert L. de Groot; Vytautas Gapsys Published in: CHemical Science, Issue 59, 2021, ISSN 2633-0679 Publisher: Royal Society of Chemistry DOI: 10.26434/chemrxiv-2021-rxxbb West-Life: A Virtual Research Environment for structural biology Author(s): Chris Morris, Paolo Andreetto, Lucia Banci, Alexandre M.J.J. Bonvin, Grzegorz Chojnowski, Laura del Cano, José Marıa Carazo, Pablo Conesa, Susan Daenke, George Damaskos, Andrea Giachetti, Natalie E.C. Haley, Maarten L. Hekkelman, Philipp Heuser, Robbie P. Joosten, Daniel Kouřil, Aleš Křenek, Tomáš Kulhánek, Victor S. Lamzin, Nurul Nadzirin, Anastassis Perrakis, Antonio Rosato, Fiona Sander Published in: Journal of Structural Biology: X, Issue 1, 2019, Page(s) 100006, ISSN 2590-1524 Publisher: Elsevier Inc. DOI: 10.1016/j.yjsbx.2019.100006 BIOACTIVE CONFORMATIONAL ENSEMBLE SERVER AND DATABASE. A PUBLIC FRAMEWORK TO SPEED UP IN SILICO DRUG DISCOVERY Author(s): Sanja Zivanovic, Genís Bayarri, Francesco Colizzi, David Moreno, Josep Lluis Gelpi, Robert Soliva, Adam Hospital, Modesto Orozco Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.0c00305 A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids Author(s): Sebastian Arangundy-Franklin, Alexander I. Taylor, Benjamin T. Porebski, Vito Genna, Sew Peak-Chew, Alexandra Vaisman, Roger Woodgate, Modesto Orozco, Philipp Holliger Published in: Nature Chemistry, Issue 11/6, 2019, Page(s) 533-542, ISSN 1755-4330 Publisher: Nature Publishing Group DOI: 10.1038/s41557-019-0255-4 The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. Author(s): Federica Battistini; Pablo D. Dans; Pablo D. Dans; Montserrat Terrazas; Chiara Lara Castellazzi; Guillem Portella; Mireia Labrador; Núria Villegas; Isabelle Brun-Heath; Carlos González; Modesto Orozco Published in: nlmid: 101238922, Issue 18, 2021, ISSN 1553-734X Publisher: Public Library of Science DOI: 10.17863/cam.79747 VeriNA3d: an R package for nucleic acids data mining Author(s): Diego Gallego, Leonardo Darré, Pablo D Dans, Modesto Orozco Published in: Bioinformatics, Issue 35/24, 2019, Page(s) 5334-5336, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btz553 Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics Author(s): Francesco Colizzi, Adam Hospital, Sanja Zivanovic, Modesto Orozco Published in: Angewandte Chemie International Edition, Issue 58/12, 2019, Page(s) 3759-3763, ISSN 1433-7851 Publisher: John Wiley & Sons Ltd. DOI: 10.1002/anie.201810922 Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors Author(s): Tomas Bastys, Vytautas Gapsys, Hauke Walter, Eva Heger, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina Published in: Retrovirology, Issue 17/1, 2020, ISSN 1742-4690 Publisher: BioMed Central DOI: 10.1186/s12977-020-00520-6 Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems Author(s): Zeynep Kurkcuoglu, Alexandre M. J. J. Bonvin Published in: Proteins: Structure, Function, and Bioinformatics, Issue 88/2, 2019, Page(s) 292-306, ISSN 0887-3585 Publisher: Wiley-Liss Inc DOI: 10.1002/prot.25802 Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4 Author(s): Vicky Charitou; Siri C. van Keulen; Alexandre M. J. J. Bonvin Published in: Crossref, Issue 78, 2022, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.2c00075 Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server Author(s): Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin Published in: Bioinformatics, Issue 35/9, 2018, Page(s) 1585-1587, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/bty816 DFFR: A NEW METHOD FOR HIGH-THROUGHPUT RECALIBRATION OF AUTOMATIC FORCE-FIELDS FOR DRUGS Author(s): David Moreno, Sanja Zivanovic, Francesco Colizzi, Adam Hospital, Juan Aranda, Robert Soliva, Modesto Orozco Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.0c00306 Large scale relative protein ligand binding affinities using non-equilibrium alchemy Author(s): Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot Published in: Chemical Science, Issue 11/4, 2020, Page(s) 1140-1152, ISSN 2041-6520 Publisher: Royal Society of Chemistry DOI: 10.1039/c9sc03754c Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope Author(s): Laura Orellana, Amy H. Thorne, Rafael Lema, Johan Gustavsson, Alison D. Parisian, Adam Hospital, Tiago N. Cordeiro, Pau Bernadó, Andrew M. Scott, Isabelle Brun-Heath, Erik Lindahl, Webster K. Cavenee, Frank B. Furnari, Modesto Orozco Published in: Proceedings of the National Academy of Sciences, Issue 116/20, 2019, Page(s) 10009-10018, ISSN 0027-8424 Publisher: National Academy of Sciences DOI: 10.1073/pnas.1821442116 MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry Author(s): Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Martin P. Bircher, Paolo Carloni, Ursula Rothlisberger Published in: Journal of Chemical Theory and Computation, Issue 15/6, 2019, Page(s) 3810-3823, ISSN 1549-9618 Publisher: American Chemical Society DOI: 10.1021/acs.jctc.9b00093 PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes Author(s): Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone Published in: Bioinformatics, Issue 35/22, 2019, Page(s) 4821-4823, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btz437 Molecular Dynamics Simulation of Amorphous Poly(3-hexylthiophene) Author(s): Flora D. Tsourtou, Loukas D. Peristeras, Rossen Apostolov, Vlasis G. Mavrantzas Published in: Macromolecules, 2020, ISSN 0024-9297 Publisher: American Chemical Society DOI: 10.1021/acs.macromol.0c00454 iScore: a novel graph kernel-based function for scoring protein–protein docking models Author(s): Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin, Li C Xue Published in: Bioinformatics, Issue 36/1, 2019, Page(s) 112-121, ISSN 1367-4803 Publisher: Oxford University Press DOI: 10.1093/bioinformatics/btz496 Structural biology in the clouds: The WeNMR-EOSC Ecosystem. Author(s): R. Vargas Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin. Published in: Frontiers in Molecular Biosciences, Issue 8, 2021, ISSN 2296-889X Publisher: Frontiers Media S.A. DOI: 10.3389/fmolb.2021.729513 Molecular Basis of CLC Antiporter Inhibition by Fluoride. Author(s): Maria Gabriella Chiariello; Viacheslav Bolnykh; Emiliano Ippoliti; Simone Meloni; Jógvan Magnus Haugaard Olsen; Thomas L. Beck; Ursula Rothlisberger; Christoph Fahlke; Paolo Carloni Published in: JACS, Issue 67, 2020, ISSN 0002-7863 Publisher: American Chemical Society DOI: 10.1021/jacs.9b13588 Book chapters (3) Accurate Calculation of Free Energy Changes upon Amino Acid Mutation Author(s): Matteo Aldeghi, Bert L. de Groot, Vytautas Gapsys Published in: Computational Methods in Protein Evolution, Issue 1851, 2019, Page(s) 19-47, ISBN 978-1-4939-8735-1 Publisher: Springer New York DOI: 10.1007/978-1-4939-8736-8_2 Managing Failures in Task-Based Parallel Workflows in Distributed Computing Environments Author(s): Jorge Ejarque, Marta Bertran, Javier Álvarez Cid-Fuentes, Javier Conejero, Rosa M. Badia Published in: Euro-Par 2020: Parallel Processing - 26th International Conference on Parallel and Distributed Computing, Warsaw, Poland, August 24–28, 2020, Proceedings, Issue 12247, 2020, Page(s) 411-425, ISBN 978-3-030-57674-5 Publisher: Springer International Publishing DOI: 10.1007/978-3-030-57675-2_26 Protein–Protein Modeling Using Cryo-EM Restraints Author(s): Mikael Trellet, Gydo van Zundert, Alexandre M. J. J. Bonvin Published in: Structural Bioinformatics - Methods and Protocols, Issue 2112, 2020, Page(s) 145-162, ISBN 978-1-0716-0269-0 Publisher: Springer US DOI: 10.1007/978-1-0716-0270-6_11 Other (3) A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver Author(s): F. Ambrosetti, Zuzana Jandova and A.M.J.J. Bonvin Published in: 2020 Publisher: arvix DOI: 10.48550/arXiv.2005.03283 proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking Author(s): F. Ambrosetti, T.H. Olsed, P.P. Olimpieri, B. Jiménez-García, E. Milanetti, P. Marcatilli and A.M.J.J. Bonvin Published in: bioRxiv, 2020, ISSN 0362-4331 Publisher: New York Times Company DOI: 10.1101/2020.03.18.967828 Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size' Author(s): V. Gapsys and B.L. de Groot Published in: 2019, ISSN 2050-084X Publisher: eLife: Accelerating discovery DOI: 10.7554/elife.44718.001 Searching for OpenAIRE data... There was an error trying to search data from OpenAIRE No results available
