BioExcel Centre of Excellence for ComputationalBiomolecular Research

Livrables

Public release of all current code development within the project, with accompanying documentation, tests, benchmarks, and benchmark reports.

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.

Final release of demonstration workflows

This deliverable will present in detail the demonstration workflows implemented, including feedback considerations, usability, availability and results.

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.

Data Management Plan

The data management plan for the use cases

Publications

The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry

Auteurs: 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
Publié dans: Chem, Numéro 5/6, 2019, Page(s) 1619-1631, ISSN 2451-9294
Éditeur: Elsevier
DOI: 10.1016/j.chempr.2019.04.002

A molecular mechanism for transthyretin amyloidogenesis

Auteurs: 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
Publié dans: Nature Communications, Numéro 10/1, 2019, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-08609-z

Computational approaches to therapeutic antibody design: established methods and emerging trends

Auteurs: Richard A Norman, Francesco Ambrosetti, Alexandre M J J Bonvin, Lucy J Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk
Publié dans: Briefings in Bioinformatics, 2019, ISSN 1467-5463
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbz095

LightDock goes information-driven

Auteurs: Jorge Roel-Touris, Alexandre M J J Bonvin, Brian Jiménez-García
Publié dans: Bioinformatics, Numéro 36/3, 2019, Page(s) 950-952, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz642

Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3

Auteurs: Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
Publié dans: Journal of Computer-Aided Molecular Design, Numéro 33/1, 2019, Page(s) 83-91, ISSN 0920-654X
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10822-018-0148-4

An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45

Auteurs: 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
Publié dans: Proteins: Structure, Function, and Bioinformatics, Numéro 88/8, 2020, Page(s) 1029-1036, ISSN 0887-3585
Éditeur: Wiley-Liss Inc
DOI: 10.1002/prot.25869

Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond

Auteurs: Alexandra Balaceanu, Diana Buitrago, Jürgen Walther, Adam Hospital, Pablo D Dans, Modesto Orozco
Publié dans: Nucleic Acids Research, Numéro 47/9, 2019, Page(s) 4418-4430, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz255

Molywood: streamlining the design and rendering of molecular movies

Auteurs: Miłosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco
Publié dans: Bioinformatics, 2020, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btaa584

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Auteurs: 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
Publié dans: Structure, Numéro 27/12, 2019, Page(s) 1745-1759, ISSN 2352-0124
Éditeur: Elsevier Limited
DOI: 10.1016/j.str.2019.11.002

An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations

Auteurs: Antonija Kuzmanic, Pablo D. Dans, Modesto Orozco
Publié dans: Chem, Numéro 5/3, 2019, Page(s) 649-663, ISSN 2451-9294
Éditeur: Elsevier
DOI: 10.1016/j.chempr.2018.12.007

A multifunctional toolkit for target-directed cancer therapy

Auteurs: Montserrat Terrazas, Dani Sánchez, Federica Battistini, Núria Villegas, Isabelle Brun-Heath, Modesto Orozco
Publié dans: Chemical Communications, Numéro 55/6, 2019, Page(s) 802-805, ISSN 1359-7345
Éditeur: Royal Society of Chemistry
DOI: 10.1039/c8cc08823c

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations

Auteurs: Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin
Publié dans: Proteins: Structure, Function, and Bioinformatics, Numéro 87/2, 2019, Page(s) 110-119, ISSN 0887-3585
Éditeur: Wiley-Liss Inc
DOI: 10.1002/prot.25630

Natural helix 9 mutants of PPARγ differently affect its transcriptional activity

Auteurs: 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
Publié dans: Molecular Metabolism, Numéro 20, 2019, Page(s) 115-127, ISSN 2212-8778
Éditeur: 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

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 47/12, 2019, Page(s) 6519-6537, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz406

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

Auteurs: Pablo D. Dans, Diego Gallego, Alexandra Balaceanu, Leonardo Darré, Hansel Gómez, Modesto Orozco
Publié dans: Chem, Numéro 5/1, 2019, Page(s) 51-73, ISSN 2451-9294
Éditeur: Elsevier
DOI: 10.1016/j.chempr.2018.09.015

Integrative Modelling of Biomolecular Complexes

Auteurs: P.I. Koukos, A.M.J.J. Bonvin
Publié dans: Journal of Molecular Biology, Numéro 432/9, 2020, Page(s) 2861-2881, ISSN 0022-2836
Éditeur: 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

Auteurs: 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
Publié dans: ACS Chemical Biology, Numéro 14/8, 2019, Page(s) 1751-1759, ISSN 1554-8929
Éditeur: 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

Auteurs: Emanuele G. Coci, Vytautas Gapsys, Natasha Shur, Yoon Shin‐Podskarbi, Bert L. Groot, Kathryn Miller, Jerry Vockley, Neal Sondheimer, Rebecca Ganetzky, Peter Freisinger
Publié dans: Human Mutation, Numéro 40/6, 2019, Page(s) 816-827, ISSN 1059-7794
Éditeur: John Wiley & Sons Inc.
DOI: 10.1002/humu.23742

Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

Auteurs: Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher, Emiliano Ippoliti, Paolo Carloni, Ursula Rothlisberger
Publié dans: Journal of Chemical Theory and Computation, Numéro 15/10, 2019, Page(s) 5601-5613, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.9b00424

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Auteurs: 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
Publié dans: F1000Research, Numéro 9, 2020, Page(s) 278, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.20559.1

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches

Auteurs: Matteo Aldeghi, Vytautas Gapsys, Bert L. de Groot
Publié dans: ACS Central Science, Numéro 5/8, 2019, Page(s) 1468-1474, ISSN 2374-7943
Éditeur: ACS Central Science
DOI: 10.1021/acscentsci.9b00590

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition

Auteurs: Federica Battistini, Adam Hospital, Diana Buitrago, Diego Gallego, Pablo D. Dans, Josep Lluis Gelpí, Modesto Orozco
Publié dans: Journal of Molecular Biology, Numéro 431/19, 2019, Page(s) 3845-3859, ISSN 0022-2836
Éditeur: 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.

Auteurs: Marie Lycksell; Urska Rovsnik; Cathrine Bergh; Nicolai Tidemand Johansen; Anne L. Martel; Lionel Porcar; Lise Arleth; Rebecca J. Howard; Erik Lindahl; Erik Lindahl
Publié dans: 'Proceedings of the National Academy of Sciences ', vol: 118 , pages: e2108006118-1-e2108006118-9 (2021), Numéro 75, 2021, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2108006118

The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Auteurs: 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
Publié dans: eLife, Numéro 9, 2020, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.53514

Pre-exascale computing of protein-ligand binding free energies with open source software for drug design.

Auteurs: Vytautas Gapsys; David F. Hahn; Gary Tresadern; David L. Mobley; Markus Rampp; Bert L. de Groot
Publié dans: Journal of Chemical Information and Modeling, Numéro 62, 2021, ISSN 1549-9596
Éditeur: 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

Auteurs: Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Publié dans: Journal of Computer-Aided Molecular Design, Numéro 34/2, 2020, Page(s) 149-162, ISSN 0920-654X
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10822-019-00244-6

The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 47/21, 2019, Page(s) 11090-11102, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz905

Surviving the deluge of biosimulation data

Auteurs: Adam Hospital, Federica Battistini, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco
Publié dans: WIREs Computational Molecular Science, Numéro 10/3, 2020, ISSN 1759-0876
Éditeur: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1449

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Auteurs: 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,
Publié dans: Proteins: Structure, Function, and Bioinformatics, Numéro 87/12, 2019, Page(s) 1200-1221, ISSN 0887-3585
Éditeur: 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

Auteurs: Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga
Publié dans: Journal of Computer-Aided Molecular Design, Numéro 33/12, 2019, Page(s) 1031-1043, ISSN 0920-654X
Éditeur: 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

Auteurs: Satu Mustalahti, Dmitry Morozov, Hoi Ling Luk, Rajanish R. Pallerla, Pasi Myllyperkiö, Mika Pettersson, Petri M. Pihko, Gerrit Groenhof
Publié dans: The Journal of Physical Chemistry Letters, Numéro 11/6, 2020, Page(s) 2177-2181, ISSN 1948-7185
Éditeur: American Chemical Society
DOI: 10.1021/acs.jpclett.0c00060

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape

Auteurs: Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Publié dans: Journal of Chemical Information and Modeling, Numéro 59/4, 2019, Page(s) 1515-1528, ISSN 1549-9596
Éditeur: American Chemical Society
DOI: 10.1021/acs.jcim.8b00730

Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling

Auteurs: 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
Publié dans: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021), Numéro 45, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Auteurs: 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.
Publié dans: Processes, Numéro 9(1), 2021, Page(s) 71, ISSN 2227-9717
Éditeur: MDPI
DOI: 10.3390/pr9010071

Mode of action of teixobactins in cellular membranes

Auteurs: 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
Publié dans: Nature Communications, Numéro 11/1, 2020, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-020-16600-2

EXPLORING THE CONFORMATIONAL LANDSCAPE OF BIOACTIVE SMALL MOLECULES

Auteurs: Sanja Zivanovic, Francesco Colizzi, David Moreno, Adam Hospital, Robert Soliva, Modesto Orozco
Publié dans: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
Éditeur: 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?

Auteurs: Cunliang Geng, Li C. Xue, Jorge Roel-Touris, Alexandre M. J. J. Bonvin
Publié dans: Wiley Interdisciplinary Reviews: Computational Molecular Science, Numéro 9/5, 2019, Page(s) e1410, ISSN 1759-0876
Éditeur: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1410

An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases

Auteurs: Juan Aranda, Montserrat Terrazas, Hansel Gómez, Núria Villegas, Modesto Orozco
Publié dans: Nature Catalysis, Numéro 2/6, 2019, Page(s) 544-552, ISSN 2520-1158
Éditeur: Nature
DOI: 10.1038/s41929-019-0290-y

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Auteurs: 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
Publié dans: Journal of Computer-Aided Molecular Design, Numéro 34/5, 2020, Page(s) 601-633, ISSN 0920-654X
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10822-020-00290-5

Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK

Auteurs: Jorge Roel-Touris, Charleen G. Don, Rodrigo V. Honorato, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
Publié dans: Journal of Chemical Theory and Computation, Numéro 15/11, 2019, Page(s) 6358-6367, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.9b00310

Molecular Basis of CLC Antiporter Inhibition by Fluoride

Auteurs: Maria Gabriella Chiariello, Viacheslav Bolnykh, Emiliano Ippoliti, Simone Meloni, Jógvan Magnus Haugaard Olsen, Thomas Beck, Ursula Rothlisberger, Christoph Fahlke, Paolo Carloni
Publié dans: Journal of the American Chemical Society, Numéro 142/16, 2020, Page(s) 7254-7258, ISSN 0002-7863
Éditeur: American Chemical Society
DOI: 10.1021/jacs.9b13588

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor

Auteurs: 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
Publié dans: Nature Communications, Numéro 10/1, 2019, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-09923-2

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Auteurs: Yuriy Khalak; Gary Tresadern; Matteo Aldeghi; Hannah Magdalena Baumann; David L. Mobley; Bert L. de Groot; Vytautas Gapsys
Publié dans: CHemical Science, Numéro 59, 2021, ISSN 2633-0679
Éditeur: Royal Society of Chemistry
DOI: 10.26434/chemrxiv-2021-rxxbb

West-Life: A Virtual Research Environment for structural biology

Auteurs: 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
Publié dans: Journal of Structural Biology: X, Numéro 1, 2019, Page(s) 100006, ISSN 2590-1524
Éditeur: 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

Auteurs: Sanja Zivanovic, Genís Bayarri, Francesco Colizzi, David Moreno, Josep Lluis Gelpi, Robert Soliva, Adam Hospital, Modesto Orozco
Publié dans: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.0c00305

A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids

Auteurs: Sebastian Arangundy-Franklin, Alexander I. Taylor, Benjamin T. Porebski, Vito Genna, Sew Peak-Chew, Alexandra Vaisman, Roger Woodgate, Modesto Orozco, Philipp Holliger
Publié dans: Nature Chemistry, Numéro 11/6, 2019, Page(s) 533-542, ISSN 1755-4330
Éditeur: Nature Publishing Group
DOI: 10.1038/s41557-019-0255-4

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.

Auteurs: 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
Publié dans: nlmid: 101238922, Numéro 18, 2021, ISSN 1553-734X
Éditeur: Public Library of Science
DOI: 10.17863/cam.79747

VeriNA3d: an R package for nucleic acids data mining

Auteurs: Diego Gallego, Leonardo Darré, Pablo D Dans, Modesto Orozco
Publié dans: Bioinformatics, Numéro 35/24, 2019, Page(s) 5334-5336, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz553

Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

Auteurs: Francesco Colizzi, Adam Hospital, Sanja Zivanovic, Modesto Orozco
Publié dans: Angewandte Chemie International Edition, Numéro 58/12, 2019, Page(s) 3759-3763, ISSN 1433-7851
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201810922

Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors

Auteurs: Tomas Bastys, Vytautas Gapsys, Hauke Walter, Eva Heger, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina
Publié dans: Retrovirology, Numéro 17/1, 2020, ISSN 1742-4690
Éditeur: 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

Auteurs: Zeynep Kurkcuoglu, Alexandre M. J. J. Bonvin
Publié dans: Proteins: Structure, Function, and Bioinformatics, Numéro 88/2, 2019, Page(s) 292-306, ISSN 0887-3585
Éditeur: Wiley-Liss Inc
DOI: 10.1002/prot.25802

Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4

Auteurs: Vicky Charitou; Siri C. van Keulen; Alexandre M. J. J. Bonvin
Publié dans: Crossref, Numéro 78, 2022, ISSN 1549-9618
Éditeur: 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

Auteurs: Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin
Publié dans: Bioinformatics, Numéro 35/9, 2018, Page(s) 1585-1587, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty816

DFFR: A NEW METHOD FOR HIGH-THROUGHPUT RECALIBRATION OF AUTOMATIC FORCE-FIELDS FOR DRUGS

Auteurs: David Moreno, Sanja Zivanovic, Francesco Colizzi, Adam Hospital, Juan Aranda, Robert Soliva, Modesto Orozco
Publié dans: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.0c00306

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

Auteurs: Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Publié dans: Chemical Science, Numéro 11/4, 2020, Page(s) 1140-1152, ISSN 2041-6520
Éditeur: 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

Auteurs: 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
Publié dans: Proceedings of the National Academy of Sciences, Numéro 116/20, 2019, Page(s) 10009-10018, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1821442116

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

Auteurs: Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Martin P. Bircher, Paolo Carloni, Ursula Rothlisberger
Publié dans: Journal of Chemical Theory and Computation, Numéro 15/6, 2019, Page(s) 3810-3823, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.9b00093

PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes

Auteurs: Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone
Publié dans: Bioinformatics, Numéro 35/22, 2019, Page(s) 4821-4823, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz437

Molecular Dynamics Simulation of Amorphous Poly(3-hexylthiophene)

Auteurs: Flora D. Tsourtou, Loukas D. Peristeras, Rossen Apostolov, Vlasis G. Mavrantzas
Publié dans: Macromolecules, 2020, ISSN 0024-9297
Éditeur: American Chemical Society
DOI: 10.1021/acs.macromol.0c00454

iScore: a novel graph kernel-based function for scoring protein–protein docking models

Auteurs: Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin, Li C Xue
Publié dans: Bioinformatics, Numéro 36/1, 2019, Page(s) 112-121, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz496

Structural biology in the clouds: The WeNMR-EOSC Ecosystem.

Auteurs: R. Vargas Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin.
Publié dans: Frontiers in Molecular Biosciences, Numéro 8, 2021, ISSN 2296-889X
Éditeur: Frontiers Media S.A.
DOI: 10.3389/fmolb.2021.729513

Molecular Basis of CLC Antiporter Inhibition by Fluoride.

Auteurs: Maria Gabriella Chiariello; Viacheslav Bolnykh; Emiliano Ippoliti; Simone Meloni; Jógvan Magnus Haugaard Olsen; Thomas L. Beck; Ursula Rothlisberger; Christoph Fahlke; Paolo Carloni
Publié dans: JACS, Numéro 67, 2020, ISSN 0002-7863
Éditeur: American Chemical Society
DOI: 10.1021/jacs.9b13588

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

Auteurs: Matteo Aldeghi, Bert L. de Groot, Vytautas Gapsys
Publié dans: Computational Methods in Protein Evolution, Numéro 1851, 2019, Page(s) 19-47, ISBN 978-1-4939-8735-1
Éditeur: Springer New York
DOI: 10.1007/978-1-4939-8736-8_2

Managing Failures in Task-Based Parallel Workflows in Distributed Computing Environments

Auteurs: Jorge Ejarque, Marta Bertran, Javier Álvarez Cid-Fuentes, Javier Conejero, Rosa M. Badia
Publié dans: Euro-Par 2020: Parallel Processing - 26th International Conference on Parallel and Distributed Computing, Warsaw, Poland, August 24–28, 2020, Proceedings, Numéro 12247, 2020, Page(s) 411-425, ISBN 978-3-030-57674-5
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-030-57675-2_26

Protein–Protein Modeling Using Cryo-EM Restraints

Auteurs: Mikael Trellet, Gydo van Zundert, Alexandre M. J. J. Bonvin
Publié dans: Structural Bioinformatics - Methods and Protocols, Numéro 2112, 2020, Page(s) 145-162, ISBN 978-1-0716-0269-0
Éditeur: Springer US
DOI: 10.1007/978-1-0716-0270-6_11

A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver

Auteurs: F. Ambrosetti, Zuzana Jandova and A.M.J.J. Bonvin
Publié dans: 2020
Éditeur: arvix
DOI: 10.48550/arXiv.2005.03283

proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking

Auteurs: F. Ambrosetti, T.H. Olsed, P.P. Olimpieri, B. Jiménez-García, E. Milanetti, P. Marcatilli and A.M.J.J. Bonvin
Publié dans: bioRxiv, 2020, ISSN 0362-4331
Éditeur: 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'

Auteurs: V. Gapsys and B.L. de Groot
Publié dans: 2019, ISSN 2050-084X
Éditeur: eLife: Accelerating discovery
DOI: 10.7554/elife.44718.001

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