List of publications

This page lists all publications with BioExcel acknowledgements or authors. See also the publication category for abstracts and previews of each publication.

2022

Stian Soiland-Reyes, Peter Sefton, Mercè Crosas, Leyla Jael Castro, Frederik Coppens, José M. Fernández, Daniel Garijo, Björn Grüning, Marco La Rosa, Simone Leo, Eoghan Ó Carragáin, Marc Portier, Ana Trisovic, RO-Crate Community, Paul Groth, Carole Goble (2022):
Packaging research artefacts with RO-Crate.
Data Science 5(2)
https://doi.org/10.3233/DS-210053

Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble (2022):
Ten simple rules for making a software tool workflow-ready.
PLOS Computational Biology 18(3)
https://doi.org/10.1371/journal.pcbi.1009823

Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes (2022):
The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00134

Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital, Paul Groth (2022):
Making Canonical Workflow Building Blocks interoperable across workflow languages.
Data Intelligence 4(2)
https://doi.org/10.1162/dint_a_00135

Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The CWL Community (2022):
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.
Communications of the ACM 65(6)
https://doi.org/10.1145/3486897

Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot (2022):
Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design.
Journal of Chemical Information and Modeling 62(5)
https://doi.org/10.1021/acs.jcim.1c01445

Vladimir Mironov, Irina A. Shchugoreva, Polina V. Artyushenko, Dmitry Morozov, Nicola Borbone, Giorgia Oliviero, Tatiana N. Zamay, Roman V. Moryachkov, Olga S. Kolovskaya, Kirill A. Lukyanenko, Yanling Song, Iuliia A. Merkuleva, Vladimir N. Zabluda, Georgy Peters, Lyudmila S. Koroleva, Dmitry V. Veprintsev, Yury E. Glazyrin, Ekaterina A. Volosnikova, Svetlana V. Belenkaya, Tatiana I. Esina, Anastasiya A. Isaeva, Valentina S. Nesmeyanova, Daniil V. Shanshin, Anna N. Berlina, Nadezhda S. Komova, Valery A. Svetlichnyi, Vladimir N. Silnikov, Dmitriy N. Shcherbakov, Galina S. Zamay, Sergey S. Zamay, Tatyana Smolyarova, Elena P. Tikhonova, Kelvin H.-C. Chen, U-Ser Jeng, Gerolama Condorelli, Vittorio de Franciscis, Gerrit Groenhof, Chaoyong Yang, Alexander A. Moskovsky, Dmitri G. Fedorov, Felix N. Tomilin, Weihong Tan, Yuri Alexeev, Maxim V. Berezovski, Anna S. Kichkailo (2022):
Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers.
Chemistry Europe 28(12)
https://doi.org/10.1002/chem.202104481

Genís Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluís Gelpí (2022):
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools.
Bioinformatics 38(12)
https://doi.org/10.1093/bioinformatics/btac316

Nícia Rosário-Ferreira, Alexandre M. J. J. Bonvin, Irina S. Moreira (2022):
Using machine-learning-driven approaches to boost hot-spot’s knowledge.
WIREs Computational Molecular Science
https://doi.org/10.1002/wcms.1602 [not Open Access]

Tim Neijenhuis, Siri C. van Keulen, Alexandre M.J. J.Bonvin (2022):
Interface refinement of low- to medium-resolution Cryo-EM complexes using HADDOCK2.4.
Structure 30(4)
https://doi.org/10.1016/j.str.2022.02.001

Rosa M. Badia, Javier Conejero, Jorge Ejarque, Daniele Lezzi, Francesc Lordan 2022
PyCOMPSs as an instrument for Translational Computer Science.
Computing in Science and Engineering 24(2)
https://doi.org/10.1109/MCSE.2022.3152945

Vicky Charitou, Siri C. van Keulen, Alexandre M.J.J. Bonvin (2022):
Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4.
Journal of Chemical Theory and Computation 18(6)
https://doi.org/10.1021/acs.jctc.2c00075

Aristarc Suriñach, Adam Hospital, Yvonne Westermaier, Luis Jordà, Sergi Orozco-Ruiz, Daniel Beltrán, Francesco Colizzi, Pau Andrio, Robert Soliva, Martí Municoy, Josep Lluís Gelpí, Modesto Orozco (2022):
Prediction Of The Impact Of Genetic Variability On Drug Sensitivity For Clinically Relevant EGFR Mutations.
bioRxiv
https://doi.org/10.1101/2022.04.25.489389

Barbara Garofalo, Alexandre M.J.J. Bonvin, Andrea Bosin, Francesco P. Di Giorgio, Rosella Ombrato, Attilio V. Vargiu (2022):
Molecular Insights Into Binding and Activation of the Human KCNQ2 Channel by Retigabine.
Frontiers in Molecular Biosciences 9
https://doi.org/10.3389/fmolb.2022.839249

Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys (2022):
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design.
Journal of Chemical Information and Modeling 62 7
https://doi.org/10.1021/acs.jcim.2c00044

Yuxuan Zhuang, Colleen M Noviello, Ryan E Hibbs, Rebecca J Howard, Erik Lindahl (2022):
Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators.
bioRxiv
https://doi.org/10.1101/2022.04.08.487470

Genís Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluís Gelpí (2022):
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations.
Nucleic Acids Research 50(W1)
https://doi.org/10.1093/nar/gkac380

Milosz Wieczor, Vito Gena, Juan Aranda, Rosa M. Badia, Josep Lluis Gelpi, Vytautas Gapsys, Bert L. de Groot, Erik Lindahl, Adam Hospital, Modesto Orozco (2022):
Pre-Exascale HPC- approaches for Molecular Dynamics simulations. Covid-19 research: a use case.
WIREs Computational Molecular Science
https://doi.org/10.1002/wcms.1622

Sandro Barissi, Alba Sala, Milosz Wieczor, Federica Battistini, Modesto Orozco (2022):
DNAffinity: A machine-learning approach to predict DNA binding affinities of transcription factors
Nucleic Acids Research
https://doi.org/10.1093/nar/gkac708

Vito Genna, Milosz Wiekzor, Adam Hospital, Modesto Orozco (2022):
Evolutionary Path and Host-selection Mechanism of SARS-CoV-2
(preprint)
https://bioexcel.eu/bioexcel-whitepaper-on-scientific-software-development-bioexcel-2-update/

Mark J. Abraham, Rossen Apostolov, Paul Bauer, Alexandre M.J.J. Bonvin, João M. Correia Teixeira, Bert L. de Groot, Vytautas Gapsys, Gerrit Groenhof, Berk Hess, Erwin Laure, Erik Lindahl, Adrien S.J. Melquiond, Dmitry Morozov, João P.G.L.M. Rodrigues, Mikael Trellet, Rodrigo Vargas Honorato (2022):
BioExcel Whitepaper on Scientific Software Development. (BioExcel-2 update)
Zenodo
https://doi.org/10.5281/zenodo.6404474

Dmitry Morozov, Vaibhav Modi, Vladimir Mironov, Gerrit Groenhof (2022):
The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization
The Journal of Physical Chemistry Letters 13(20)
https://doi.org/10.1021/acs.jpclett.2c00899

Ruth Tichauer, Dmitry Morozov, Ilia Sokolovskii, Jussi Toppari, Gerrit Groenhof (2022):
Identifying Vibrations that Control Non-adiabatic Relaxation of Polaritons In Strongly Coupled Molecule-Cavity Systems
The Journal of Physical Chemistry Letters 13
https://doi.org/10.1021/acs.jpclett.2c00826

Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L de Groot, Vytautas Gapsys (2022):
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design
Journal of Chemical Information and Modeling 62(7)
https://doi.org/10.1021/acs.jcim.2c00044

Jorge Ejarque, Pau Andrio, Adam Hospital, Javier Conejero, Daniele Lezzi, Josep LL. Gelpi, Rosa M. Badia (2022):
The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows
IEEE 18th International Conference on eScience (eScience 2022)
(accepted)
Preprint: https://doi.org/10.48550/arXiv.2208.14130

Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist, Bert de Groot, Vytautas Gapsys (2022):
Automated relative binding free energy calculations: from SMILES to ΔΔG
ChemRxiv
https://doi.org/10.26434/chemrxiv-2022-vqbxg

Pavel Buslaev, Noora Aho, Anton Jansen, Paul Bauer, Berk Hess, Gerrit Groenhof (2022):
Best practices in constant pH MD simulations: accuracy and sampling
ChemRxiv
https://doi.org/10.26434/chemrxiv-2022-c6lg2

Charles J. Buchanan, Ben Gaunt, Peter J. Harrison, Yun Yang, Jiwei Liu, Aziz Khan, Andrew M. Giltrap, Audrey Le Bas, Philip N. Ward, Kapil Gupta, Maud Dumoux, Tiong Kit Tan, Lisa Schimaski, Sergio Daga, Nicola Picchiotti, Margherita Baldassarri, Elisa Benetti, Chiara Fallerini, Francesca Fava, Annarita Giliberti, Panagiotis I. Koukos, Matthew J. Davy, Abirami Lakshminarayanan, Xiaochao Xue, Georgios Papadakis, Lachlan P. Deimel, Virgínia Casablancas-Antràs, Timothy D. W. Claridge, Alexandre M. J. J. Bonvin, Quentin J. Sattentau, Simone Furini, Marco Gori, Jiandong Huo, Raymond J. Owens, Christiane Schaffitzel, Imre Berger, Alessandra Renieri, James H. Naismith, Andrew J. Baldwin, Benjamin G. Davis (2022):
Pathogen-sugar interactions revealed by universal saturation transfer analysis
Science 377
https://doi.org/10.1126/science.abm3125

Rhythm Shukla, Francesca Lavore, Sourav Maity, Maik G. N. Derks, Chelsea R. Jones, Bram J. A. Vermeulen, Adéla Melcrová, Michael A. Morris, Lea  Marie Becker, Xiaoqi Wang, Raj Kumar, João Medeiros-Silva, Roy A. M. van Beekveld, Alexandre M. J. J. Bonvin, Joseph H. Lorent, Moreno Lelli,  James S. Nowick, Harold D. MacGillavry, Aaron J. Peoples, Amy L.  Spoering, Losee L. Ling, Dallas E. Hughes, Wouter H. Roos, Eefjan  Breukink, Kim Lewis, Markus Weingarth (2022):
Teixobactin kills bacteria by a two-pronged attack on the cell envelope
Nature 608:7922
https://doi.org/10.1038/s41586-022-05019-y

Marie Lycksell, Urška Rovšnik, Anton Hanke, Anne Martel, Rebecca J Howard, Erik Lindahl (2022):
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
bioRxiv
https://doi.org/10.1101/2022.05.06.490775

2021

Tobias Kuhn, Vincent Emonet, Haris Antonatos, Stian Soiland-Reyes, Michel Dumontier (2021):
Semantic micro-contributions with decentralized nanopublication services
PeerJ Computer Science 7:e387
https://doi.org/10.7717/peerj-cs.387

Robert Dods, Petra Båth, Dmitry Morozov, Viktor Ahlberg Gagnér, David Arnlund, Hoi Ling Luk, Joachim Kübel, Michał Maj, Adams Vallejos, Cecilia Wickstrand, Robert Bosman, Kenneth R. Beyerlein, Garrett Nelson, Mengning Liang, Despina Milathianaki, Joseph Robinson, Rajiv Harimoorthy, Peter Berntsen, Erik Malmerberg, Linda Johansson, Rebecka Andersson, Sergio Carbajo, Elin Claesson, Chelsie E. Conrad, Peter Dahl, Greger Hammarin, Mark S. Hunter, Chufeng Li, Stella Lisova, Antoine Royant, Cecilia Safari, Amit Sharma, Garth J. Williams, Oleksandr Yefanov, Sebastian Westenhoff, Jan Davidsson, Daniel P. DePonte, Sébastien Boutet, Anton Barty, Gergely Katona, Gerrit Groenhof, Gisela Brändén, Richard Neutze (2021):
Ultrafast structural changes within a photosynthetic reaction centre.
Nature 589(7841)
https://doi.org/10.1038/s41586-020-3000-7 [preprint]

Martin Werner, Vytautas Gapsys, Bert L de Groot (2021):
One Plus One Makes Three: Triangular Coupling of Correlated Amino Acid Mutations
The Journal of Physical Chemistry Letters 12
https://doi.org/10.1021/acs.jpclett.1c00380  

Yuriy Khalak, Gary Tresadern, Bert L de Groot, Vytautas Gapsys (2021):
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software
Journal of Computer-aided Molecular Design 35(1)
https://doi.org/10.1007/s10822-020-00359-1

Hannah M Baumann, Vytautas Gapsys, Bert L de Groot, David L Mobley (2021):
Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations
The Journal of Physical Chemistry B 125(17)
https://doi.org/10.1021/acs.jpcb.0c10263 [deposited version]

Vytautas Gapsys, Ahmet Yildirim, Matteo Aldeghi, Yuriy Khalak, David Van der Spoel, Bert L de Groot (2021):
Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
Communications Chemistry 4(1)
https://doi.org/10.1038/s42004-021-00498-y

Charlotte W. van Noort, Rodrigo V. Honorato, Alexandre M.J.J. Bonvin (2021):
Information-Driven Modeling of Biomolecular Complexes
Current Opinion in Structural Biology 70
https://doi.org/10.1016/j.sbi.2021.05.003

Gytis Dudas, Samuel L. Hong, Barney I. Potter, Sébastien Calvignac-Spencer, Frédéric S. Niatou-Singa, Thais B. Tombolomako, Terence Fuh-Neba, Ulrich Vickos, Markus Ulrich, Fabian H. Leendertz, Kamran Khan, Carmen Huber, Alexander Watts, Ingrida Olendraitė, Joost Snijder, Kim N. Wijnant, Alexandre M.J.J. Bonvin, Pascale Martres, Sylvie Behillil, Ahidjo Ayouba, Martin Foudi Maidadi, Dowbiss Meta Djomsi, Celestin Godwe, Christelle Butel, Aistis Šimaitis, Miglė Gabrielaitė, Monika Katėnaitė, Rimvydas Norvilas, Ligita Raugaitė, Giscard Wilfried Koyaweda, Jephté Kaleb Kandou, Rimvydas Jonikas, Inga Nasvytienė, Živilė Žemeckienė, Dovydas Gečys, Kamilė Tamušauskaitė, Milda Norkienė, Emilija Vasiliūnaitė, Danguolė Žiogienė, Albertas Timinskas, Marius Šukys, Mantas Šarauskas, Gediminas Alzbutas, Adrienne Amuri Aziza, Eddy Kinganda Lusamaki, Jean-Claude Makangara Cigolo, Francisca Muyembe Mawete, Emmanuel Lokilo Lofiko, Placide Mbala Kingebeni, Jean-Jacques Muyembe Tamfum, Marie Roseline Darnycka Belizaire, René Ghislain Essomba, Marie Claire Okomo Assoumou, Akenji Blaise Mboringong, Alle Baba Dieng, Dovilė Juozapaitė, Salome Hosch, Justino Obama, Mitoha Ondo’o Ayekaba, Daniel Naumovas, Arnoldas Pautienius, Clotaire Donatien Rafaï, Astra Vitkauskienė, Rasa Ugenskienė, Alma Gedvilaitė, Darius Čereškevičius, Vaiva Lesauskaitė, Lukas Žemaitis, Laimonas Griškevičius, Guy Baele (2021):
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Nature Communications 12(1)
https://doi.org/10.1038/s41467-021-26055-8

Heidi L. Rehm, Angela J. H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J. S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K. Bonfield, Tiffany F. Boughtwood, Guillaume Bourque, Sarion R. Bowers, Anthony J. Brookes, Michael Brudno, Matthew H. Brush, David Bujold, Tony Burdett, Orion J. Buske, Moran N. Cabili, Daniel L. Cameron, Robert J. Carroll, Esmeralda Casas-Silva, Debyani Chakravarty, Bimal P. Chaudhari, Shu Hui Chen, J. Michael Cherry, Justina Chung, Melissa Cline, Hayley L. Clissold, Robert M. Cook-Deegan, Mélanie Courtot, Fiona Cunningham, Miro Cupak, Robert M. Davies, Danielle Denisko, Megan J. Doerr, Lena I. Dolman, Edward S. Dove, L. Jonathan Dursi, Stephanie O. M. Dyke, James A. Eddy, Karen Eilbeck, Kyle P. Ellrott, Susan Fairley, Khalid A. Fakhro, Helen V. Firth, Michael S. Fitzsimons, Marc Fiume, Paul Flicek, Ian M. Fore, Mallory A. Freeberg, Robert R. Freimuth, Lauren A. Fromont, Jonathan Fuerth, Clara L. Gaff, Weiniu Gan, Elena M. Ghanaim, David Glazer, Robert C. Green, Malachi Griffith, Obi L. Griffith, Robert L. Grossman, Tudor Groza, Jaime M. Guidry Auvil, Roderic Guigó, Dipayan Gupta, Melissa A. Haendel, Ada Hamosh, David P. Hansen, Reece K. Hart, Dean Mitchell Hartley, David Haussler, Rachele M. Hendricks-Sturrup, Calvin W. L. Ho, Ashley E. Hobb, Michael M. Hoffman, Oliver M. Hofmann, Petr Holub, Jacob Shujui Hsu, Jean-Pierre Hubaux, Sarah E. Hunt, Ammar Husami, Julius O. Jacobsen, Saumya S. Jamuar, Elizabeth L. Janes, Francis Jeanson, Aina Jené, Amber L. Johns, Yann Joly, Steven J. M. Jones, Alexander Kanitz, Kazuto Kato, Thomas M. Keane, Kristina Kekesi-Lafrance, Jerome Kelleher, Giselle Kerry, Seik-Soon Khor, Bartha M. Knoppers, Melissa A. Konopko, Kenjiro Kosaki, Martin Kuba, Jonathan Lawson, Rasko Leinonen, Stephanie Li, Michael F. Lin, Mikael Linden, Xianglin Liu, Isuru Udara Liyanage, Javier Lopez, Anneke M. Lucassen, Michael Lukowski, Alice L. Mann, John Marshall, Michele Mattioni, Alejandro Metke-Jimenez, Anna Middleton, Richard J. Milne, Fruzsina Molnár-Gábor, Nicola Mulder, Monica C. Munoz-Torres, Rishi Nag, Hidewaki Nakagawa, Jamal Nasir, Arcadi Navarro, Tristan H. Nelson, Ania Niewielska, Amy Nisselle, Jeffrey Niu, Tommi H. Nyrönen, Brian D. O’Connor, Sabine Oesterle, Soichi Ogishima, Vivian Ota Wang, Laura A. D. Paglione, Emilio Palumbo, Helen E. Parkinson, Anthony A. Philippakis, Angel D. Pizarro, Andreas Prlic, Jordi Rambla, Augusto Rendon, Renee A. Rider, Peter N. Robinson, Kurt W. Rodarmer, Laura Lyman Rodriguez, Alan F. Rubin, Manuel Rueda, Gregory A. Rushton, Rosalyn S. Ryan, Gary I. Saunders, Helen Schuilenburg, Torsten Schwede, Serena Scollen, Alexander Senf, Nathan C. Sheffield, Neerjah Skantharajah, Albert V. Smith, Heidi J. Sofia, Dylan Spalding, Amanda B. Spurdle, Zornitza Stark, Lincoln D. Stein, Makoto Suematsu, Patrick Tan, Jonathan A. Tedds, Alastair A. Thomson, Adrian Thorogood, Timothy L. Tickle, Katsushi Tokunaga, Juha Törnroos, David Torrents, Sean Upchurch, Alfonso Valencia, Roman Valls Guimera, Jessica Vamathevan, Susheel Varma, Danya F. Vears, Coby Viner, Craig Voisin, Alex H. Wagner, Susan E. Wallace, Brian P. Walsh, Marc S. Williams, Eva C. Winkler, Barbara J. Wold, Grant M. Wood, J. Patrick Woolley, Chisato Yamasaki, Andrew D. Yates, Christina K. Yung, Lyndon J. Zass, Ksenia Zaytseva, Junjun Zhang, Peter Goodhand, Kathryn North, Ewan Birney (2021):
GA4GH: International policies and standards for data sharing across genomic research and healthcare
Cell Genomics 1(2)
https://doi.org/10.1016/j.xgen.2021.100029

Sheikh Nizamuddin, Stefanie Koidl, Tanja Bhuiyan, Tamara V Werner, Martin L Biniossek, Alexandre M J J Bonvin, Silke Lassmann, HThMarc Timmers (2021):
Integrating quantitative proteomics with accurate genome profiling of transcription factors by greenCUT&RUN
Nucleic Acids Research 49(9)
https://doi.org/10.1093/nar/gkab038

Nicolas Renaud, Cunliang Geng, Sonja Georgievska, Francesco Ambrosetti, Lars Ridder, Dario F. Marzella, Manon F. Réau, Alexandre M. J. J. Bonvin, Li C. Xue  (2021):
DeepRank: A deep learning framework for data mining 3D protein-protein interfaces
Nature Communications 12(1)
https://doi.org/10.1038/s41467-021-27396-0

Zuzana Jandova, Attilio Vittorio Vargiu, Alexandre M. J. J. Bonvin (2021):
Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
Journal of Chemical Theory and Computation 17(9)
https://doi.org/10.1021/acs.jctc.1c00336   

Charles J. Buchanan, Ben Gaunt, Peter J. Harrison, Yun Yang, Jiwei Liu, Aziz Khan, Andrew M. Giltrap, Audrey Le Bas, Philip N. Ward, Kapil Gupta, Maud Dumoux, Sergio Daga, Nicola Picchiotti, Margherita Baldassarri, Elisa Benetti, Chiara Fallerini, Francesca Fava, Annarita Giliberti, Panagiotis I. Koukos, Abirami Lakshminarayanan, Xiaochao Xue, Georgios Papadakis, Lachlan P. Deimel, Virgínia Casablancas-Antràs, Timothy D.W. Claridge, Alexandre M.J.J. Bonvin, Quentin J. Sattentau, Simone Furini, Marco Gori, Jiandong Huo, Raymond J. Owens, Christiane Schaffitzel, Imre Berger, Alessandra Renieri, GEN-COVID Multicenter Study, James H. Naismith, Andrew Baldwin, Benjamin G. Davis, J.H. Naismith, A. Baldwin, B.G. Davis (2021):
Cryptic SARS-CoV2-spike-with-sugar interactions revealed by ‘universal’ saturation transfer analysis.
bioRxiv
https://doi.org/10.1101/2021.04.14.439284

Panagiotis I. Koukos, Manon Réau, Alexandre M. J. J. Bonvin (2021):
Shape-restrained modelling of protein-small molecule complexes with HADDOCK
Journal of Chemical Information and Modeling 61(9)
https://doi.org/10.1021/acs.jcim.1c00796

Marc F. Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A. G. Chaleil, Tereza Clarence, Paul A. Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S. Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka G. Lipska, Adam Liwo, Emilia A. Lubecka, Martyna Maszota‐Zieleniak, Adam K. Sieradzan, Rafał Ślusarz, Patryk A. Wesołowski, Karolina Zięba, Carlos A. Del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J. Gray, Alexandre M. J. J. Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jiménez‐García, Panagiotis I. Koukos, Siri Van Keulen, Charlotte W. Van Noort, Manon Réau, Jorge Roel‐Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A. Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A. Rodríguez‐Lumbreras, Juan Fernandez‐Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng‐You Huang, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G. Pierce, Didier Barradas‐Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda‐Shitaka, Petras J. Kundrotas, Amar Singh, Ilya A. Vakser, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J. Wodak (2021):
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment
Proteins: Structure, Function, and Bioinformatics 89(12)
https://doi.org/10.1002/prot.26222  [preprint ]

Y. Khalak, G. Tresadern, M. Aldeghi, H. M. Baumann, D. L. Mobley, B. L. de Groot, V. Gapsys (2021):
Alchemical absolute protein–ligand binding free energies for drug design.
Chemical Science 12(41)
https://doi.org/10.1039/D1SC03472C

Dmitry Morozov, Vladimir Mironov, Roman V. Moryachkov, Irina A. Shchugoreva, Polina V. Artyushenko, Galina S. Zamay, Olga S. Kolovskaya, Tatiana N. Zamay, Alexey V. Krat, Dmitry S. Molodenskiy, Vladimir N. Zabluda, Dmitry V. Veprintsev, Alexey E. Sokolov, Ruslan A. Zukov, Maxim V. Berezovski, Felix N. Tomilin, Dmitri G. Fedorov, Yuri Alexeev, Anna S. Kichkail (2021):
The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
Molecular Therapy – Nucleic Acids 25
https://doi.org/10.1016/j.omtn.2021.07.015  

Elina Multamäki, Rahul Nanekar, Dmitry Morozov, Topias Lievonen, David Golonka, Weixiao Yuan Wahlgren, Brigitte Stucki-Buchli, Jari Rossi, Vesa P. Hytönen, Sebastian Westenhoff, Janne A. Ihalainen, Andreas Möglich, Heikki Takala  (2021):
Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling
Nature Communications 12
https://doi.org/10.1038/s41467-021-24676-7

Genís Bayarri, Adam Hospital, Modesto Orozco (2021):
3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories
Frontiers in Molecular Biosciences 8
https://doi.org/10.3389/fmolb.2021.726232  

Cathrine Bergh, Stephanie A Heusser, Rebecca Howard, Erik Lindahl (2021):
Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel
eLife 10
https://doi.org/10.7554/eLife.68369

Urška Rovšnik, Yuxuan Zhuang, Björn O Forsberg, Marta Carroni, Linnea Yvonnesdotter, Rebecca J Howard, Erik Lindahl  (2021):
Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations
Life Science Alliance 4(8)
https://doi.org/10.26508/lsa.202101011  

Pau Andrio, Adam Hospital, Cristian Ramon-Cortes, Javier Conejero, Daniele Lezzi, Jorge Ejarque, Josep LL. Gelpi, Rosa M. Badia (2021):
Enabling the execution of large scale workflows for molecular dynamics simulations
bioRxiv
https://doi.org/10.1101/2021.04.14.439795

Federica Battistini, Pablo D. Dans, Montserrat Terrazas, Chiara L. Castellazzi, Guillem Portella, Mireia Labrador, Núria Villegas, Isabelle Brun-Heath, Carlos González, Modesto Orozco (2021):
The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function
PLOS Computational Biology 17(11)
https://doi.org/10.1371/journal.pcbi.1009547

Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft  (2021):
Perspectives on automated composition of workflows in the life sciences
F1000Research 10
https://doi.org/10.12688/f1000research.54159.1

Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Ilkay Altintas, Rosa M Badia, Bartosz Balis, Tainã Coleman, Frederik Coppens, Frank Di Natale, Bjoern Enders, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Daniel Garijo, Carole Goble, Dorran Howell, Shantenu Jha, Daniel S. Katz, Daniel Laney, Ulf Leser, Maciej Malawski, Kshitij Mehta, Loïc Pottier, Jonathan Ozik, J. Luc Peterson, Lavanya Ramakrishnan, Stian Soiland-Reyes, Douglas Thain, Matthew Wolf (2021):
A Community Roadmap for Scientific Workflows Research and Development
2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS)
https://doi.org/10.1109/WORKS54523.2021.00016 [preprint]

Rudolf Wittner, Petr Holub, Heimo Müller, Jörg Geiger, Carole Goble, Stian Soiland-Reyes, Luca Pirredu, Francesca Frexia, Cecilia Mascia, Elliot Fairweather, Jason R. Swedlow, Josh Moore, Caterina Strambio, Gianluigi Zanetti, David Grunwald, Hiroki Nakae (2021):
ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen and Data
In: Provenance and Annotation of Data and Processes. IPAW 2020, IPAW 2021.
Lecture Notes in Computer Science
12839
https://doi.org/10.1007/978-3-030-80960-7_16 [preprint]

Carole Goble, Stian Soiland-Reyes, Finn Bacall, Stuart Owen, Alan Williams, Ignacio Eguinoa, Bert Droesbeke, Simone Leo, Luca Pireddu, Laura Rodriguez-Navas, José Mª Fernández, Salvador Capella-Gutierrez, Hervé Ménager, Björn Grüning, Beatriz Serrano-Solano, Philip Ewels, Frederik Coppens (2021):
Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory
Zenodo
https://doi.org/10.5281/zenodo.4605654

Yong Jung, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue, Vasant G. Honavar (2021):
MetaScore: A novel machine-learning based approach to improve traditional scoring functions for scoring protein-protein docking conformations
bioRxiv
https://doi.org/10.1101/2021.10.06.463442

2020

Mustalahti, D. Morozov, H. L. Luk, R. R. Pallerla, P. Myllyperkiö, M. Pettersson, P. Pihko, G. Groenhof (2020):
Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond is Locked.
The Journal of Physical Chemistry Letters 11(6)
https://doi.org/10.1021/acs.jpclett.0c00060

Claesson, W. Y. Wahlgren, H. Takala, S. Pandey, L. Castillon, V. Kuznetsova, L. Henry, M. Panman, M. Carrillo, J. Kuebel, R. Nanekar, L. Isaksson, A. Nimmrich, A. Cellini, D. Morozov, M. Maj, M. Kurttila, R. Bosman, E. Nango, R. Tanaka, T. Tanaka, L. Fangjia, S. Iwata, S. Owada, K. Moffat, G. Groenhof, E. A. Stojkovic, J. A. Ihalainen, M. Schmidt, S. Westenhoff (2020):
The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser.
eLife 9
https://doi.org/10.7554/eLife.53514

Flora Tsourtou, Loukas D. Peristeras, Rossen Apostolov, Vlasis G. Mavrantzas (2020):
Molecular dynamics simulation of amorphous poly(3-hexylthiophene).
Macromolecules 53(18)
https://doi.org/10.1021/acs.macromol.0c00454  [not Open Access]

M.G. Chiariello, V. Bolnykh, E. Ippoliti, S. Meloni, J. M. Haugaard Olsen, T. Beck, U. Rothlisberger, C. Fahlke, P. Carloni (2020):
Molecular Basis of CLC Antiporter Inhibition by Fluoride.
Journal of the American Chemical Society 142(16)
https://doi.org/10.1021/jacs.9b13588 [preprint]

Bolnykh, J. M. Haugaard Olsen, S. Meloni, M. P. Bircher, E. Ippoliti, P. Carloni, U. Rothlisberger (2020):
MiMiC: Multiscale Modeling in Computational Chemistry.
Frontiers in Molecular Biosciences 7:45
https://doi.org/10.3389/fmolb.2020.00045

Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L de Groot (2020):
Large scale relative protein ligand binding affinities using non-equilibrium alchemy.
Chemical Science 11
https://doi.org/10.1039/c9sc03754c

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 (2020):
The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations.
Journal of Computer-Aided Molecular Design 34
https://doi.org/10.1007/s10822-020-00290-5 [preprint]

M.E. Trellet, G. van Zundert, A.M.J.J. Bonvin. (2020):
Protein–Protein Modeling Using Cryo-EM Restraints.
Methods in Molecular Biology 2112
https://doi.org/10.1007/978-1-0716-0270-6_11 [preprint]

J.L. Roel Touris, A.M.J.J. Bonvin, B. Jimenez-Garcia (2020):
LightDock goes information-driven.
Bioinformatics 36(3)
https://doi.org/10.1093/bioinformatics/btz642

Ambrosetti, B. Jiménez-García, J. Roel-Touris, A.M.J.J. Bonvin. (2020):
Modeling Antibody-Antigen Complexes by Information-Driven Docking.
Structure 28(1)
https://doi.org/10.1016/j.str.2019.10.011

Basciu, P.I. Koukos, G. Malloci, A.M.J.J. Bonvin, A.V. Vargiu (2020):
Coupling enhanced sampling of the apo‐receptor with template‐based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4.
Journal of Computer-Aided Molecular Design 34
https://doi.org/10.1007/s10822-019-00244-6 [preprint]

Zeynep Kurkcuoglu, Alexandre M. J. J. Bonvin (2020):
Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.
Proteins: Structure, Function, and Bioinformatics 88(2)
https://doi.org/10.1002/prot.25802

P.I. Koukos, J. Roel-Touris, F. Ambrosetti, C. Geng, J. Schaarschmidt, M.E. Trellet, A.S.J. Melquiond, L.C. Xue, R.V. Honorato, I. Moreira, Z. Kurkcuoglu, A. Vangone, A.M.J.J. Bonvin. (2020):
An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45.
Proteins: Structure, Function, and Bioinformatics 88(1)
https://doi.org/10.1002/prot.25869

Ambrosetti, T.H. Olsed, P.P. Olimpieri, B. Jiménez-García, E. Milanetti, P. Marcatilli, A.M.J.J. Bonvin (2020):
proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking.
Bioinformatics 36(20)
https://doi.org/10.1093/bioinformatics/btaa644

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 Schneider (2020):
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 3 approved with reservations].
F1000 Research 9(278)
https://doi.org/10.12688/f1000research.20559.1

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 (2020):
Mode of action of teixobactins in cellular conditions.
Nature Communication 11(1):2848
https://doi.org/10.1038/s41467-020-16600-2

Francesco Ambrosetti, Zuzana Jandova, Alexandre M.J.J. Bonvin (2020):
A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver
arXiv
https://doi.org/10.48550/arXiv.2005.03283

Jorge Ejarque, Marta Bertran, Javier Álvarez Cid-Fuentes, Javier Conejero, Rosa M. Badia (2020):
Managing Failures in task-based parallel workflows in distributed computing environments
In: Euro-Par 2020: Euro-Par 2020: Parallel Processing,
Lecture Notes in Computer Science
12247
https://doi.org/10.1007/978-3-030-57675-2_26 [preprint]

Tomas Bastys, Vytautas Gapsys, Hauke Walter, Eva Heger, Nadezhda T Doncheva, Rolf Kaiser, Bert L de Groot, Olga V Kalinina (2020):
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors
Retrovirology 17:13
https://doi.org/10.1186/s12977-020-00520-6

Sanja Zivanovic, Genis Bayarri, Francesco Colizzi, David Moreno, Josep Lluis Gelpí, Robert Soliva, Adam Hospital, Modesto Orozco (2020):
Bioactive Conformational Ensemble Server And Database. A Public Framework To Speed Up In Silico Drug Discovery.
Journal of Chemical Theory and Computation 16(10)
https://doi.org/10.1021/acs.jctc.0c00305 [preprint]

Sanja Zivanovic, Francesco Colizzi, David Moreno, Adam Hospital, Robert Soliva, Modesto Orozco (2020):
Exploring The Conformational Landscape Of Bioactive Small Molecules
Journal of Chemical Theory and Computation 16(10)
https://doi.org/10.1021/acs.jctc.0c00304 [preprint]

Miłosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco (2020):
Molywood: streamlining the design and rendering of molecular movies
Bioinformatics 36(17)
https://doi.org/10.1093/bioinformatics/btaa584

David Moreno, Sanja Zivanovic, Francesco Colizzi, Adam Hospital, Juan Aranda, Robert Soliva, Modesto Orozco (2020):
DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs
Journal of Chemical Theory and Computation 16(10)
https://doi.org/10.1021/acs.jctc.0c00306 [preprint]

Alexander Leitner, Alexandre M.J.J. Bonvin, Christoph H. Borchers, Robert J. Chalkley, Julia Chamot-Rooke, Colin W. Combe, Jürgen Cox, Meng-Qiu Dong, Lutz Fischer, Michael Götze, Fabio C. Gozzo, Albert J. R. Heck, Michael R. Hoopmann, Lan Huang, Yasushi Ishihama, Andrew R. Jones, Nir Kalisman, Oliver Kohlbacher, Karl Mechtler, Robert L. Moritz, Eugen Netz, Petr Novak, Evgeniy Petrotchenko, Andrej Sali, Richard A. Scheltema, Carla Schmidt, David Schriemer, Andrea Sinz, Frank Sobott, Florian Stengel, Konstantinos Thalassinos, Henning Urlaub, Rosa Viner, Juan A. Vizcaino, Marc R. Wilkins, Juri Rappsilber (2020):
Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry
Structure 28(11)
https://doi.org/10.1016/j.str.2020.09.011

Jorge Roel-Touris,  Brian Jiménez-García,  Alexandre M.J.J. Bonvin (2020):
Integrative Modeling of Membrane-associated Protein Assemblies
Nature Communications 11:6210
https://doi.org/10.1038/s41467-020-20076-5

Giulia Palermo, Alexandre M. J. J. Bonvin, Matteo Dal Peraro, Rommie E. Amaro, Valentina Tozzini (2020):
Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
Frontiers in Molecular Biosciences 7:194
https://doi.org/10.3389/fmolb.2020.00194

Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober (2020):
FAIR Computational Workflows
Data Intelligence 2(1–2):43862
https://doi.org/10.1162/dint_a_00033

Nick Juty, Sarala M. Wimalaratne, Stian Soiland-Reyes, John Kunze, Carole A. Goble, Tim Clark (2020):
Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR
Data Intelligence 2(1–2):43862
https://doi.org/10.1162/dint_a_00025  

Annika Jacobsen, Ricardo de Miranda Azevedo, Nick Juty, Dominique Batista, Simon Coles, Ronald Cornet, Mélanie Courtot, Mercè Crosas, Michel Dumontier, Chris T. Evelo, Carole Goble, Giancarlo Guizzardi, Karsten Kryger Hansen, Ali Hasnain, Kristina Hettne, Jaap Heringa, Rob W.W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias Kuhn, Ignasi Labastida, Barbara Magagna, Peter McQuilton, Natalie Meyers, Annalisa Montesanti, Mirjam van Reisen, Philippe Rocca-Serra, Robert Pergl, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Juliane Schneider, George Strawn, Mark Thompson, Andra Waagmeester, Tobias Weigel, Mark D. Wilkinson, Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes (2020):
FAIR Principles: Interpretations and Implementation Considerations
Data Intelligence 2(1–2):43862
https://doi.org/10.1162/dint_r_00024  

Paul Groth, Helena Cousijn, Tim Clark, Carole Goble (2020):
FAIR Data Reuse – the Path through Data.
Data Intelligence 2(1–2):43862
https://doi.org/10.1162/dint_a_00030  

Gerrit Groenhof, Vaibhav Modi, Dmitry Morozov (2020):
Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations
Current Opinion in Structural Biology 61
https://doi.org/10.1016/j.sbi.2019.12.013

Guillem Portella, Modesto Orozco, Michele Vendruscolo (2020):
Determination of a structural ensemble representing the dynamics of a G-quadruplex DNA
Biochemistry 59(4)
https://doi.org/10.1021/acs.biochem.9b00493 [preprint]

Akshay Sridhar, Stephen E. Farr, Guillem Portella, Tamar Schlick, Modesto Orozco, Rosana Collepardo-Guevara (2020):
Dependence of chromatin hierarchical looping on protein disorder and nucleosome asymmetry
Proceedings of the National Academy of Sciences 117(13)
https://doi.org/10.1073/pnas.1910044117

Jürgen Walther, Pablo D Dans, Alexandra Balaceanu, Adam Hospital, Genís Bayarri, Modesto Orozco (2020):
A Multi-Modal Coarse-Grain Model of DNA Flexibility Mappable to the Atomistic Level
Nucleic Acids Research 48(5)
https://doi.org/10.1093/nar/gkaa015

Akshay Sridhar, Modesto Orozco, Rosana Collepardo-Guevara (2020):
Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1.
Nucleic Acids Research 48(10)
https://doi.org/10.1093/nar/gkaa285

Paulina J. Dziubańska-Kusibab, Hilmar Berger, Federica Battistini, Britta A. M. Bouwman, Amina Iftekhar, Riku Katainen, Tatiana Cajuso, Nicola Crosetto, Modesto Orozco, Lauri A. Aaltonen, Thomas F. Meyer (2020):
Collibactin DNA damage signature indicates mutational impact in colorectal cancer
Nature Medicine 26(7)
https://doi.org/10.1038/s41591-020-0908-2 [preprint] [preprint #2]

Satish Sati, Boyan Bonev, Quentin Szabo, Daniel Jost, Paul Bensadoun, Francois Serra, Vincent Loubiere, Giorgio Lucio Papadopoulos, Juan-Carlos Rivera-Mulia, Lauriane Fritsch, Pauline Bouret, David Castillo, Josep Ll. Gelpi, Modesto Orozco, Cedric Vaillant, Franck Pellestor, Frederic Bantignies, Marc A. Marti-Renom, David M. Gilbert, Jean-Marc Lemaitre, Giacomo Cavalli (2020):
4D Genome rewiring during oncogene-induced and replicative senescence
Molecular Cell 78(3)
https://doi.org/10.1016/j.molcel.2020.03.007

Robert Dods, Petra Båth, Dmitry Morozov, Viktor Ahlberg Gagnér, David Arnlund, Hoi Ling Luk, Joachim Kübel, Michał Maj, Adams Vallejos, Cecilia Wickstrand, Robert Bosman, Kenneth R. Beyerlein, Garrett Nelson, Mengning Liang, Despina Milathianaki, Joseph Robinson, Rajiv Harimoorthy, Peter Berntsen, Erik Malmerberg, Linda Johansson, Rebecka Andersson, Sergio Carbajo, Elin Claesson, Chelsie E. Conrad, Peter Dahl, Greger Hammarin, Mark S. Hunter, Chufeng Li, Stella Lisova, Antoine Royant, Cecilia Safari, Amit Sharma, Garth J. Williams, Oleksandr Yefanov, Sebastian Westenhoff, Jan Davidsson, Daniel P. DePonte, Sébastien Boutet, Anton Barty, Gergely Katona, Gerrit Groenhof, Gisela Brändén, Richard Neutze (2020):
Ultrafast structural changes within a photosynthetic reaction centre
Nature 589
https://doi.org/10.1038/s41586-020-3000-7 [preprint]

Vytautas Gapsys, Bert L de Groot (2020):
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size.
eLife 9
https://doi.org/10.7554/eLife.57589   

Yong Wang, Joseph A Lyons, Milena Timcenko, Bert L de Groot, Poul Nissen, Vytautas Gapsys, Kresten Lindorff-Larsen (2020):
Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase
bioRxiv
https://doi.org/10.1101/2020.06.24.169771   

2019

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 (2019):
A molecular mechanism for transthyretin amyloidogenesis
Nature Communications 10
https://doi.org/10.1038/s41467-019-08609-z

Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone (2019):
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes
Bioinformatics 35(22)
https://doi.org/10.1093/bioinformatics/btz437

Levi N. Naden, Sam Ellis, Shantenu Jha (2019):
MolSSI and BioExcel Workflow Workshop 2018 Report
arXiv
https://doi.org/10.48550/arXiv.1905.11863

Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Martin P. Bircher, Paolo Carloni, Ursula Rothlisberger (2019):
MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry
Journal of Chemical Theory and Computation 15 (6)
https://doi.org/10.1021/acs.jctc.9b00093 [preprint]

Matteo Aldeghi, Bert L. de Groot, Vytautas Gapsys (2019):
Accurate Calculation of Free Energy Changes upon Amino Acid Mutation
In: Computational Methods in Protein Evolution,
Methods in Molecular Biology 1851
https://doi.org/10.1007/978-1-4939-8736-8_2 [preprint]

Emanuele G. Coci, Vytautas Gapsys, Natasha Shur, Yoon Shin‐Podskarbi, Bert L. Groot, Kathryn Miller, Jerry Vockley, Neal Sondheimer, Rebecca Ganetzky, Peter Freisinger (2019):
Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype–phenotype correlation
Human mutation 40 (6)
https://doi.org/10.1002/humu.23742 [author’s deposit]

Vytautas Gapsys, Bert L de Groot (2019):
Comment on ’Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size’
eLife 8
https://doi.org/10.7554/eLife.44718.001

A. Vangone, J. Schaarschmidt, P. Koukos, C. Geng, N. Citro, M.E. Trellet, L.C. Xue, A.M.J.J. Bonvin (2019):
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.
Bioinformatics 35(9)
https://doi.org/10.1093/bioinformatics/bty816

Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin(2019):
Protein-ligand pose and affinity prediction. Lessons from D3R Grand Challenge 3
Journal of Computer-Aided Molecular Design 33 (1)
https://doi.org/10.1007/s10822-018-0148-4

Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin (2019):
iSEE: Interface structure, evolution, and energy‐based machine learning predictor of binding affinity changes upon mutations
Proteins: Structure, Function, and Bioinformatics 87 (2)
https://doi.org/10.1002/prot.25630

Cunliang Geng, Li C. Xue, Jorge Roel‐Touris, Alexandre M. J. J. Bonvin(2019):
Finding the ∆∆G spot: Are predictors of binding affinity changes upon mutations in protein-protein interactions ready for it?
WIREs Computational Molecular Science 9(5)
https://doi.org/10.1002/wcms.1410

Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin, Li C Xue (2019):
iScore: A novel graph kernel-based function for scoring protein-protein docking models
Bioinformatics 36(1)
https://doi.org/10.1093/bioinformatics/btz496

Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu (2019):
Holo-like and druggable protein conformations from enhanced-sampling of binding pocket shape.
Journal of Chemical Information and Modeling 59 (4)
https://doi.org/10.1021/acs.jcim.8b00730

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 (2019):
Folding Then Binding vs. Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic alpha-Amylase.
ACS Chemical Biology 14(8)
https://doi.org/10.1021/acschembio.9b00290

Pablo D. Dans, Diego Gallego, Alexandra Balaceanu, Leonardo Darré, Hansel Gómez, Modesto Orozco (2019):
Modeling, simulations and bioinformatics at the service of RNA structure
Chem  5(1)
https://doi.org/10.1016/j.chempr.2018.09.015

Antonija Kuzmanic, Pablo D. Dans, Modesto Orozco (2019):
An in-depth look at DNA crystals through the prism of molecular Dynamics simulations
Chem 5(3)
https://doi.org/10.1016/j.chempr.2018.12.007

Montserrat Terrazas, Dani Sánchez, Federica Battistini, Núria Villegas, Isabelle Brun-Heathab, Modesto Orozco (2019):
A multifunctional Toolkit for target-directed cancer therapy
Chemical Communications 55(6)
https://doi.org/10.1039/C8CC08823C

Francesco Colizzi, Adam Hospital, Sanja Zivanovic, Modesto Orozco (2019):
Predicting the limit of intramolecular H-bonding with classical molecular Dynamics
Angewandte Chemie 131(12)
https://doi.org/10.1002/ange.201810922 [preprint]

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 (2019):
Oncogenic mutations in the EGFR ectodomain coverge structurally to mimic the transition State detected by mAB806
Proceedings of the National Academy of Sciences 116(20)
https://doi.org/10.1073/pnas.1821442116

Alexandra Balaceanu, Diana Buitrago, Jürgen Walther, Adam Hospital, Pablo D Dans, Modesto Orozco (2019):
Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond.
Nucleic Acids Research 47(9)
https://doi.org/10.1093/nar/gkz255

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 (2019):
The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Assymetry
Chem  5(6)
https://doi.org/10.1016/j.chempr.2019.04.002

Sebastian Arangundy-Franklin, Alexander I. Taylor, Benjamin T. Porebski, Vito Genna, Sew Peak-Chew, Alexandra Vaisman, Roger Woodgate, Modesto Orozco, Philipp Holliger (2019):
A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl-phosphonate nucleic acids
Nature Chemistry 11
https://doi.org/10.1038/s41557-019-0255-4 [preprint]

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 (2019):
Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor
Nature Communications 10
https://doi.org/10.1038/s41467-019-09923-2

Juan Aranda, Montserrat Terrazas, Hansel Gómez, Núria Villegas, Modesto Orozco (2019):
An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases
Nature Catalysis 2(6)
https://doi.org/10.1038/s41929-019-0290-y [not Open Access]

Matteo Aldeghi, Vytautas Gapsys, Bert L. de Groot (2019):
Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches
ACS Central Science
https://doi.org/10.1021/acscentsci.9b00590

Pau Andrio, Adam Hospital, Javier Conejero, Luis Jordá, Marc Del Pino, Laia Codo, Stian Soiland-Reyes, Carole Goble, Daniele Lezzi, Rosa M. Badia, Modesto Orozco, Josep Ll. Gelpi (2019):
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
Scientific Data 6(1)
https://doi.org/10.1038/s41597-019-0177-4

Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher, Emiliano Ippoliti, Paolo Carloni, Ursula Rothlisberger (2019):
Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC
Journal of Chemical Theory and Computation 15(10)
https://doi.org/10.1021/acs.jctc.9b00424 [preprint]

Emanuele G Coci, Vytautas Gapsys, Natasha Shur, Yoon Shin‐Podskarbi, Bert L de Groot, Kathryn Miller, Jerry Vockley, Neal Sondheimer, Rebecca Ganetzky, Peter Freisinger (2019):
Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype–phenotype correlation
Human Mutation 40(6)
https://doi.org/10.1002/humu.23742 [preprint]

Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L de Groot, Bogdan I Iorga (2019):
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset
Journal of Computer-Aided Molecular Design 33 (12)
https://doi.org/10.1007/s10822-019-00232-w [preprint]

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 (2019):
Natural helix 9 mutants of PPARγ differently affect its transcriptional activity
Molecular Metabolism 20
https://doi.org/10.1016/j.molmet.2018.12.005

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 Sanderson, Joan Segura, Joerg Schaarschmidt, Egor Sobolev, Sergio Traldi, Mikael E. Trellet, Sameer Velankar, Marco Verlato, Martyn Winn (2019):
West-Life: A Virtual Research Environment for structural biology.
Journal of Structural Biology: X 1
https://doi.org/10.1016/j.yjsbx.2019.100006

Richard A Norman, Francesco Ambrosetti, Alexandre M J J Bonvin, Lucy J Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk (2019):
Computational approaches to therapeutic antibody design: established methods and emerging trends.
Briefings in Bioinformatics 21(5)
https://doi.org/10.1093/bib/bbz095

Jorge Roel-Touris, Charleen G. Don, Rodrigo V. Honorato, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin (2019):
Less is more: Coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK.
Journal of Chemical Theory and Computation 15(11)
https://doi.org/10.1021/acs.jctc.9b00310

Rodrigo V. Honorato, Jorge Roel-Touris, Alexandre M. J. J. Bonvin (2019):
MARTINI-based protein-DNA coarse-grained HADDOCKing
Frontiers in Molecular Biosciences 6(102)
https://doi.org/10.3389/fmolb.2019.00102

Helen M. Berman, Paul D. Adams, Alexandre A. Bonvin, Stephen K. Burley, Bridget Carragher, Wah Chiu, Frank DiMaio, Thomas E. Ferrin, Margaret J. Gabanyi, Thomas D. Goddard, Patrick R. Griffin, Juergen Haas, Christian A. Hanke, Jeffrey C. Hoch, Gerhard Hummer, Genji Kurisu, Catherine L. Lawson, Alexander Leitner, John L. Markley, Jens Meiler, Gaetano T. Montelione, George N. Phillips, Thomas Prisner, Juri Rappsilber, David C. Schriemer, Torsten Schwede, Claus A.M. Seidel, Timothy S. Strutzenberg, Dmitri I. Svergun, Emad Tajkhorshid, Jill Trewhella, Brinda Vallat, Sameer Velankar, Geerten W. Vuister, Benjamin Webb, John D. Westbrook, Kate L. White, Andrej Sali (2019):
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures
Structure 27(12)
https://doi.org/10.1016/j.str.2019.11.002

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, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng‐You Huang, Mireia Rosell, Luis A. Rodríguez‐Lumbreras, Miguel Romero‐Durana, Lucía Díaz‐Bueno, Juan Fernandez‐Recio, Charles Christoffer, Genki Terashi, Woong‐Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathryn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain H. Moal, David W. Ritchie, Isaure Chauvot de Beauchêne, Bernard Maigret, Marie‐Dominique Devignes, Maria E. Ruiz Echartea, Didier Barradas‐Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman‐Duhovny, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Petras J. Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha D. Badal, Ilya A. Vakser, Thom Vreven, Sweta Vangaveti, Tyler Borrman, Zhiping Weng, Johnathan D. Guest, Ragul Gowthaman, Brian G. Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panagiotis I. Koukos, Jorge Roel‐Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E. Trellet, Adrien S. J. Melquiond, Li Xue, Brian Jiménez‐García, Charlotte W. Noort, Rodrigo V. Honorato, Alexandre M. J. J. Bonvin, Shoshana J. Wodak(2019):
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment.
Proteins: Structure, Function, and Bioinformatics 87(12)
https://doi.org/10.1002/prot.25838 [preprint]

P.I. Koukos and A.M.J.J. Bonvin (2019):
Integrative modelling of biomolecular complexes.
Journal of Molecular Biology 421(9)
https://doi.org/10.1016/j.jmb.2019.11.009

Federica Battistini, Adam Hospital, Diana Buitrago, Diego Gallego, Pablo D. Dans, Josep Lluis Gelpí, Modesto Orozco (2019):
How B-DNA Dynamics decipher sequence-selective protein recognition
Journal of Molecular Biology 431(19)
https://doi.org/10.1016/j.jmb.2019.07.021

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 (2019):
The static and Dynamic estructural heterogeneities of B-DNA: extending Calladine-Dickerson rules
Nucleic Acids Research 47(21)
https://doi.org/10.1093/nar/gkz905

Adam Hospital, Federica Battistini, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco (2019):
Surviving the Deluge of Biosimulation Data
WIREs Computational Molecular Science 10(3)
https://doi.org/10.1002/wcms.1449 [not Open Access]

Diego Gallego, Leonardo Darré, Pablo D Dans, Modesto Orozco (2019):
VeriNA3d: an R package for nucleic acids data mining
Bioinformatics 35(24)
https://doi.org/10.1093/bioinformatics/btz553

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 (2019):
DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region
Nucleic Acids Research 47(12)
https://doi.org/10.1093/nar/gkz406

Farah Zaib Khan, Stian Soiland-Reyes, Richard O Sinnott, Andrew Lonie, Carole Goble, Michael R Crusoe (2019):
Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv
GigaScience 8(11)
https://doi.org/10.1093/gigascience/giz095

Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin (2019):
Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
Journal of computer-aided molecular design 33
https://doi.org/10.1007/s10822-018-0148-4

2018

Anna Rubio-Cosials, Federica Battistini, Alexander Gansen, Anna Cuppari, Pau Bernadó, Modesto Orozco, Jörg Langowski, Katalin Tóth, Maria Solà (2018):
Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution.
Biophysical Journal 114
https://doi.org/10.1016/j.bpj.2017.11.3743

Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, J. P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, A. M. J. J. Bonvin (2018):
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
Journal of Computer-Aided Molecular Design 32(1)
https://doi.org/10.1007/s10822-017-0049-y

Amparo Garcia-Lopez, Francesca Tessaro, Hendrik R. A. Jonker, Anna Wacker, Christian Richter, Arnaud Comte, Nikolaos Berntenis, Roland Schmucki, Klas Hatje, Olivier Petermann, Gianpaolo Chiriano, Remo Perozzo, Daniel Sciarra, Piotr Konieczny, Ignacio Faustino, Guy Fournet, Modesto Orozco, Ruben Artero, Friedrich Metzger, Martin Ebeling, Peter Goekjian, Benoît Joseph, Harald Schwalbe, Leonardo Scapozza (2018):
Targeting RNA structure in SMNS reverses spinal muscular atrophy molecular phenotypes.
Nature Communications 9(1)
https://doi.org/10.1038/s41467-018-04110-1

Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone (2018):
Distinguishing crystallographic from biological interfa2017ces in protein complexes: Role of intermolecular contacts and energetics for classification
BMC Bioinformatics
https://doi.org/10.1186/s12859-018-2414-9

Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu (2018):
An enhanced-sampling MD-based protocol for molecular docking.
bioRxiv
https://doi.org/10.1101/434092

Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin (2018):
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.
Bioinformatics 35(9)
https://doi.org/10.1093/bioinformatics/bty816

Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin (2018):
Protein-ligand pose and affinity prediction. Lessons from D3R Grand Challenge 3.
Journal of Computer-Aided Molecular Design 33(1)
https://doi.org/10.1007/s10822-018-0148-4

Alexandre M. J. J. Bonvin, Ezgi Karaca, Panagiotis L. Kastritis, João P. G. L. M. Rodrigues (2018):
Defining distance restraints in HADDOCK
Nature Protocols 13(7)
https://doi.org/10.1038/s41596-018-0017-6

Mark J. Abraham, Adrien S.J. Melquiond, Emiliano Ippoliti, Vytautas Gapsys, Berk Hess, Mikael Trellet, João P.G.L.M. Rodrigues, Erwin Laure, Rossen Apostolov, Bert L. de Groot, Alexandre M.J.J. Bonvin, Erik Lindahl (2018):
BioExcel Whitepaper on Scientific Software Development.
Zenodo
https://doi.org/10.5281/zenodo.1194634

Tomas Bastys, Vytautas Gapsys, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina (2018):
Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations
Journal of Chemical Theory and Computation 14(7)
https://doi.org/10.1021/acs.jctc.7b01109 [preprint]

Rodolfo Briones, Christian Blau, Carsten Kutzner, Bert L. de Groot, Camilo Aponte-Santamaría (2018):
GROmaρs: a GROMACS-based toolset to analyse density maps derived from molecular dynamics simulations
Biophysical Journal 116(1)
https://doi.org/10.1016/j.bpj.2018.11.3126

Panagiotis I. Koukos, Inge Faro, Charlotte W. van Noort, Alexandre M.J.J. Bonvin (2018):
A membrane protein complex docking benchmark.
Journal of Molecular Biology 430(24)
https://doi.org/10.1016/j.jmb.2018.11.005

Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin (2018):
iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations.
Proteins: Structure, Function, and Bioinformatics 87(2)
https://doi.org/10.1002/prot.25630

Viveca Lindahl, Pontus Gourdon, Magnus Andersson, Berk Hess (2018):
Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
Scientific Reports 8(1):2995
https://doi.org/10.1038/s41598-018-21357-2

Erik Lindahl (editor in chief) (2018):
The Scientific Case for Computing in Europe 2018-2026
PRACE
ISBN 9789082169492
http://www.prace-ri.eu/third-scientific-case/

Stian Soiland-Reyes, Marcos Cáceres (2018):
The Archive and Package (arcp) URI scheme
2018 IEEE 14th International Conference on e-Science (e-Science)
https://doi.org/10.1109/eScience.2018.00018 [ preprint ]

Aldeghi, V. Gapsys, B. L. de Groot (2018):
Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation
ACS Central Science 4(12)
https://doi.org/10.1021/acscentsci.8b00717

Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder (2018):
Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results
PLOS Biology 16(12):e3000099
https://doi.org/10.1371/journal.pbio.3000099

2017

Víctor López-Ferrando, Andrea Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Ll Gelpí (2017):
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update.
Nucleic Acids Research 45(W1)
https://doi.org/10.1093/nar/gkx313

Julie A. McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K. Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C. Ison, Rafael C. Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R. McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L. Snoep, Stian Soiland-Reyes, Natalie J. Stanford, Neil Swainston, Nicole Washington, Alan R. Williams, Sarala M. Wimalaratne, Lilly M. Winfree, Katherine Wolstencroft, Carole Goble, Christopher J. Mungall, Melissa A. Haendel, Helen Parkinson (2017):
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
PLOS Biology 15(6)
https://doi.org/10.1371/journal.pbio.2001414

Adam Hospital, Michela Candotti, Josep Lluis Gelpi, Modesto Orozco (2017):
The Multiple Roles of Waters in Protein Solvation
The Journal of Physical Chemistry B
https://doi.org/10.1021/acs.jpcb.6b09676

Jinyu Li, Wenping Lyu, Giulia Rossetti, Albert Konijnenberg, Antonino Natalello, Emiliano Ippoliti, Modesto Orozco, Frank Sobott, Rita Grandori, Paolo Carloni (2017):
Proton Dynamics in Protein Mass Spectrometry.
Journal of Physical Chemistry Letters 8
https://doi.org/10.1021/acs.jpclett.7b00127

Vytautas Gapsys, Bert L. de Groot (2017):
pmx Webserver: A User Friendly Interface for Alchemistry
Journal of Chemical Information and Modelling 57(2)
https://doi.org/10.1021/acs.jcim.6b00498

G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato, A.M.J.J. Bonvin (2017):
The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes.
Journal of Molecular Biology 429(3)
https://doi.org/10.1016/j.jmb.2016.11.032

Steffen Möller, Stuart W. Prescott, Lars Wirzenius, Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matúš Kalaš, Andreas Tille, Michael R. Crusoe (2017):
Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis
Data Science and Engineering 2:232
https://doi.org/10.1007/s41019-017-0050-4

Vytautas Gapsys, Bert L. de Groot (2017):
Alchemical free energy calculations for nucleotide mutations in protein-DNA complexes
Journal of Chemical Theory and Computation 13(12)
https://doi.org/10.1021/acs.jctc.7b00849

Irina S. Moreira, Panagiotis I. Koukos, Rita Melo, Jose G. Almeida, Antonio J. Preto, Joerg Schaarschmidt, Mikael Trellet, Zeynep H. Gümüş, Joaquim Costa, Alexandre M. J. J. Bonvin (2017):
SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots.
Nature Scientific Reports 7(1)
https://doi.org/10.1038/s41598-017-08321-2

Ezgi Karaca, João P G L M Rodrigues, Andrea Graziadei, Alexandre M J J Bonvin, Teresa Carlomagno (2017):
M3: An Integrative Framework for Structure Determination of Molecular Machines.
Nature Methods 14(9)
https://doi.org/10.1038/nmeth.4392

2016

João P.G.L.M. Rodrigues, Adrien S.J. Melquiond, Alexandre M.J.J. Bonvin (2016):
Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students
Biochemistry and Molecular Biology Education 44(2)
https://doi.org/10.1002/bmb.20941

G.C.P. van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries, A.M.J.J. Bonvin (2016):
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes
Journal of Molecular Biology 428(4)
https://doi.org/10.1016/j.jmb.2015.09.014

Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de Groot (2016):
Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan
Angewandte Chemie 55(26)
https://doi.org/10.1002/anie.201510054

Pablo D Dans, Jürgen Walther, Hansel Gómez, Modesto Orozco (2016):
Multiscale simulation of DNA
Current opinions in Structural Biology 37
https://doi.org/10.1016/j.sbi.2015.11.011
http://www.ncbi.nlm.nih.gov/pubmed/26708341

Pablo D. Dans, Linda Danilāne, Ivan Ivani, Tomáš Dršata, Filip Lankaš, Adam Hospital, Jürgen Walther, Ricard Illa Pujagut, Federica Battistini, Josep Lluis Gelpí, Richard Lavery, Modesto Orozco (2016):
Long-time scale dynamics of the Drew Dickerson Dodecamer
Nucleic Acids Research 44(9)
https://doi.org/10.1093/nar/gkw264

Ardita Shkurti, Ramon Goni, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles A. Laughton (2016):
pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data.
Software X 5
https://doi.org/10.1016/j.softx.2016.04.002

Michela Candotti, Modesto Orozco (2016):
The Differential Response of Proteins to Macromolecular Crowding.
PLOS Computational Biology 12(7):e1005040
https://doi.org/10.1371/journal.pcbi.1005040

Martin Kotev, Robert Soliva, Modesto Orozco (2016):
Challenges of docking in large, flexible and promiscuous binding sites
Bioorganic & Medicinal Chemistry 24(20)
https://doi.org/10.1016/j.bmc.2016.08.010

Laura Orellana, Ozge Yoluk, Oliver Carrillo, Modesto Orozco, Erik Lindahl (2016):
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations.
Nature Communications
https://doi.org/10.1038/ncomms12575   

Dimitrios Spiliotopoulos, Panagiotis L. Kastritis, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri (2016):
dMM-PBSA: a new HADDOCK scoring function for protein-peptide docking.
Frontiers in Molecular Biosciences 3(46)
https://doi.org/10.3389/fmolb.2016.00046

Cunliang Geng, Anna Vangone, Alexandre M.J.J. Bonvin (2016):
Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes.
Protein Engineering, Design, and Selection 29
https://doi.org/10.1093/protein/gzw020

Rhys Grinter, Inokentijs Josts, Khedidja Mosbahi, Aleksander W. Roszak, Richard J. Cogdell, Alexandre M. J. J. Bonvin, Joel J. Milner, Sharon M. Kelly, Olwyn Byron, Brian O. Smith & Daniel Walker (2016):
Structure of the bacterial plant-ferredoxin receptor FusA
Nature Communications
https://doi.org/10.1038/ncomms13308

Anna Villar-Piqué, Tomás Lopes da Fonseca, Ricardo Sant’Anna, Éva Mónika Szegö, Luis Fonseca-Ornelas, Raquel Pinho, Anita Carija, Ellen Gerhardt, Caterina Masaracchia, Enrique Abad Gonzalez, Giulia Rossetti, Paolo Carloni, Claudio O. Fernández, Debora Foguel, Ira Milosevic, Markus Zweckstetter, Salvador Ventura, Tiago Fleming Outeiro (2016):
Environmental and genetic factors support the dissociation between α-synuclein aggregation and toxicity
Proceedings of the National Academy of Sciences of the United States of America 113(42)
https://doi.org/10.1073/pnas.1606791113

Eva S. Cunha, Pedro Sfriso, Adriana L. Rojas, Adam Hospital, Modesto Orozco, Nicola G.A. Abrescia,
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Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop
Structure 25(1)
https://doi.org/10.1016/j.str.2016.11.003

Kyle Chard, Mike D’ Arcy, Ben Heavner, Ian Foster, Carl Kesselman, Ravi Madduri, Alexis Rodriguez, Stian Soiland-Reyes, Carole Goble, Kristi Clark, Eric W. Deutsch, Ivo Dinov, Nathan Price, Arthur Toga (2016):
I’ll Take That to Go: Big Data Bags and Minimal Identifiers for Exchange of Large, Complex Datasets.
IEEE International Conference on Big Data 2016
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Antonis Troumpoukis, Angelos Charalambidis, Giannis Mouchakis, Stasinos Konstantopoulos, Ronald Siebes, Victor de Boer, Stian Soiland-Reyes, Daniela Digles (2016):
Developing a Benchmark Suite for Semantic Web Data from Existing Workflows
BLINK 2016 Workshop on Benchmarking Linked Data,
CEUR Workshop Proceedings 1700(04)
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https://doi.org/10.5281/zenodo.159568

Iman Pouya, Sander Pronk, Magnus Lundborg, Erik Lindahl (2016):
Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling
Future Generation Computer Systems 71
https://doi.org/10.1016/j.future.2016.11.004

Dari Kimanius, Björn O Forsberg, Sjors HW Scheres, Erik Lindahl (2016):
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
eLife 5:e18722
https://doi.org/10.7554/eLife.18722