BioExcel Centre of Excellence for ComputationalBiomolecular Research

Resultado final

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

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.

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.

Data Management Plan

The data management plan for the use cases

Publicaciones

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

Autores: 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
Publicado en: Chem, Edición 5/6, 2019, Página(s) 1619-1631, ISSN 2451-9294
Editor: Elsevier
DOI: 10.1016/j.chempr.2019.04.002

A molecular mechanism for transthyretin amyloidogenesis

Autores: 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
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-08609-z

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

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

LightDock goes information-driven

Autores: Jorge Roel-Touris, Alexandre M J J Bonvin, Brian Jiménez-García
Publicado en: Bioinformatics, Edición 36/3, 2019, Página(s) 950-952, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz642

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

Autores: Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
Publicado en: Journal of Computer-Aided Molecular Design, Edición 33/1, 2019, Página(s) 83-91, ISSN 0920-654X
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10822-018-0148-4

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

Autores: 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
Publicado en: Proteins: Structure, Function, and Bioinformatics, Edición 88/8, 2020, Página(s) 1029-1036, ISSN 0887-3585
Editor: Wiley-Liss Inc
DOI: 10.1002/prot.25869

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

Autores: Alexandra Balaceanu, Diana Buitrago, Jürgen Walther, Adam Hospital, Pablo D Dans, Modesto Orozco
Publicado en: Nucleic Acids Research, Edición 47/9, 2019, Página(s) 4418-4430, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkz255

Molywood: streamlining the design and rendering of molecular movies

Autores: Miłosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco
Publicado en: Bioinformatics, 2020, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa584

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

Autores: 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
Publicado en: Structure, Edición 27/12, 2019, Página(s) 1745-1759, ISSN 2352-0124
Editor: Elsevier Limited
DOI: 10.1016/j.str.2019.11.002

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

Autores: Antonija Kuzmanic, Pablo D. Dans, Modesto Orozco
Publicado en: Chem, Edición 5/3, 2019, Página(s) 649-663, ISSN 2451-9294
Editor: Elsevier
DOI: 10.1016/j.chempr.2018.12.007

A multifunctional toolkit for target-directed cancer therapy

Autores: Montserrat Terrazas, Dani Sánchez, Federica Battistini, Núria Villegas, Isabelle Brun-Heath, Modesto Orozco
Publicado en: Chemical Communications, Edición 55/6, 2019, Página(s) 802-805, ISSN 1359-7345
Editor: Royal Society of Chemistry
DOI: 10.1039/c8cc08823c

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

Autores: Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin
Publicado en: Proteins: Structure, Function, and Bioinformatics, Edición 87/2, 2019, Página(s) 110-119, ISSN 0887-3585
Editor: Wiley-Liss Inc
DOI: 10.1002/prot.25630

Natural helix 9 mutants of PPARγ differently affect its transcriptional activity

Autores: 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
Publicado en: Molecular Metabolism, Edición 20, 2019, Página(s) 115-127, ISSN 2212-8778
Editor: 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

Autores: 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
Publicado en: Nucleic Acids Research, Edición 47/12, 2019, Página(s) 6519-6537, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkz406

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

Autores: Pablo D. Dans, Diego Gallego, Alexandra Balaceanu, Leonardo Darré, Hansel Gómez, Modesto Orozco
Publicado en: Chem, Edición 5/1, 2019, Página(s) 51-73, ISSN 2451-9294
Editor: Elsevier
DOI: 10.1016/j.chempr.2018.09.015

Integrative Modelling of Biomolecular Complexes

Autores: P.I. Koukos, A.M.J.J. Bonvin
Publicado en: Journal of Molecular Biology, Edición 432/9, 2020, Página(s) 2861-2881, ISSN 0022-2836
Editor: 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

Autores: 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
Publicado en: ACS Chemical Biology, Edición 14/8, 2019, Página(s) 1751-1759, ISSN 1554-8929
Editor: 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

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

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

Autores: Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher, Emiliano Ippoliti, Paolo Carloni, Ursula Rothlisberger
Publicado en: Journal of Chemical Theory and Computation, Edición 15/10, 2019, Página(s) 5601-5613, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.9b00424

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

Autores: 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
Publicado en: F1000Research, Edición 9, 2020, Página(s) 278, ISSN 2046-1402
Editor: F1000 Research Ltd.
DOI: 10.12688/f1000research.20559.1

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

Autores: Matteo Aldeghi, Vytautas Gapsys, Bert L. de Groot
Publicado en: ACS Central Science, Edición 5/8, 2019, Página(s) 1468-1474, ISSN 2374-7943
Editor: ACS Central Science
DOI: 10.1021/acscentsci.9b00590

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition

Autores: Federica Battistini, Adam Hospital, Diana Buitrago, Diego Gallego, Pablo D. Dans, Josep Lluis Gelpí, Modesto Orozco
Publicado en: Journal of Molecular Biology, Edición 431/19, 2019, Página(s) 3845-3859, ISSN 0022-2836
Editor: 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.

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

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

Autores: 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
Publicado en: eLife, Edición 9, 2020, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.53514

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

Autores: Vytautas Gapsys; David F. Hahn; Gary Tresadern; David L. Mobley; Markus Rampp; Bert L. de Groot
Publicado en: Journal of Chemical Information and Modeling, Edición 62, 2021, ISSN 1549-9596
Editor: 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

Autores: Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Publicado en: Journal of Computer-Aided Molecular Design, Edición 34/2, 2020, Página(s) 149-162, ISSN 0920-654X
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10822-019-00244-6

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

Autores: 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
Publicado en: Nucleic Acids Research, Edición 47/21, 2019, Página(s) 11090-11102, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkz905

Surviving the deluge of biosimulation data

Autores: Adam Hospital, Federica Battistini, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco
Publicado en: WIREs Computational Molecular Science, Edición 10/3, 2020, ISSN 1759-0876
Editor: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1449

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

Autores: 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,
Publicado en: Proteins: Structure, Function, and Bioinformatics, Edición 87/12, 2019, Página(s) 1200-1221, ISSN 0887-3585
Editor: 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

Autores: Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga
Publicado en: Journal of Computer-Aided Molecular Design, Edición 33/12, 2019, Página(s) 1031-1043, ISSN 0920-654X
Editor: 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

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

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

Autores: Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Publicado en: Journal of Chemical Information and Modeling, Edición 59/4, 2019, Página(s) 1515-1528, ISSN 1549-9596
Editor: American Chemical Society
DOI: 10.1021/acs.jcim.8b00730

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

Autores: 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
Publicado en: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021), Edición 45, 2021, ISSN 2041-1723
Editor: Nature Publishing Group

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Autores: 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.
Publicado en: Processes, Edición 9(1), 2021, Página(s) 71, ISSN 2227-9717
Editor: MDPI
DOI: 10.3390/pr9010071

Mode of action of teixobactins in cellular membranes

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-16600-2

EXPLORING THE CONFORMATIONAL LANDSCAPE OF BIOACTIVE SMALL MOLECULES

Autores: Sanja Zivanovic, Francesco Colizzi, David Moreno, Adam Hospital, Robert Soliva, Modesto Orozco
Publicado en: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
Editor: 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?

Autores: Cunliang Geng, Li C. Xue, Jorge Roel-Touris, Alexandre M. J. J. Bonvin
Publicado en: Wiley Interdisciplinary Reviews: Computational Molecular Science, Edición 9/5, 2019, Página(s) e1410, ISSN 1759-0876
Editor: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1410

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

Autores: Juan Aranda, Montserrat Terrazas, Hansel Gómez, Núria Villegas, Modesto Orozco
Publicado en: Nature Catalysis, Edición 2/6, 2019, Página(s) 544-552, ISSN 2520-1158
Editor: Nature
DOI: 10.1038/s41929-019-0290-y

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

Autores: 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
Publicado en: Journal of Computer-Aided Molecular Design, Edición 34/5, 2020, Página(s) 601-633, ISSN 0920-654X
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10822-020-00290-5

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

Autores: Jorge Roel-Touris, Charleen G. Don, Rodrigo V. Honorato, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
Publicado en: Journal of Chemical Theory and Computation, Edición 15/11, 2019, Página(s) 6358-6367, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.9b00310

Molecular Basis of CLC Antiporter Inhibition by Fluoride

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

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

Autores: 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
Publicado en: Nature Communications, Edición 10/1, 2019, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-09923-2

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

Autores: Yuriy Khalak; Gary Tresadern; Matteo Aldeghi; Hannah Magdalena Baumann; David L. Mobley; Bert L. de Groot; Vytautas Gapsys
Publicado en: CHemical Science, Edición 59, 2021, ISSN 2633-0679
Editor: Royal Society of Chemistry
DOI: 10.26434/chemrxiv-2021-rxxbb

West-Life: A Virtual Research Environment for structural biology

Autores: 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
Publicado en: Journal of Structural Biology: X, Edición 1, 2019, Página(s) 100006, ISSN 2590-1524
Editor: 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

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

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

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

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

Autores: 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
Publicado en: nlmid: 101238922, Edición 18, 2021, ISSN 1553-734X
Editor: Public Library of Science
DOI: 10.17863/cam.79747

VeriNA3d: an R package for nucleic acids data mining

Autores: Diego Gallego, Leonardo Darré, Pablo D Dans, Modesto Orozco
Publicado en: Bioinformatics, Edición 35/24, 2019, Página(s) 5334-5336, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz553

Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

Autores: Francesco Colizzi, Adam Hospital, Sanja Zivanovic, Modesto Orozco
Publicado en: Angewandte Chemie International Edition, Edición 58/12, 2019, Página(s) 3759-3763, ISSN 1433-7851
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201810922

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

Autores: Tomas Bastys, Vytautas Gapsys, Hauke Walter, Eva Heger, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina
Publicado en: Retrovirology, Edición 17/1, 2020, ISSN 1742-4690
Editor: 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

Autores: Zeynep Kurkcuoglu, Alexandre M. J. J. Bonvin
Publicado en: Proteins: Structure, Function, and Bioinformatics, Edición 88/2, 2019, Página(s) 292-306, ISSN 0887-3585
Editor: Wiley-Liss Inc
DOI: 10.1002/prot.25802

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

Autores: Vicky Charitou; Siri C. van Keulen; Alexandre M. J. J. Bonvin
Publicado en: Crossref, Edición 78, 2022, ISSN 1549-9618
Editor: 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

Autores: Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin
Publicado en: Bioinformatics, Edición 35/9, 2018, Página(s) 1585-1587, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty816

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

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

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

Autores: Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Publicado en: Chemical Science, Edición 11/4, 2020, Página(s) 1140-1152, ISSN 2041-6520
Editor: 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

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 116/20, 2019, Página(s) 10009-10018, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.1821442116

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

Autores: Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Martin P. Bircher, Paolo Carloni, Ursula Rothlisberger
Publicado en: Journal of Chemical Theory and Computation, Edición 15/6, 2019, Página(s) 3810-3823, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.9b00093

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

Autores: Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone
Publicado en: Bioinformatics, Edición 35/22, 2019, Página(s) 4821-4823, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz437

Molecular Dynamics Simulation of Amorphous Poly(3-hexylthiophene)

Autores: Flora D. Tsourtou, Loukas D. Peristeras, Rossen Apostolov, Vlasis G. Mavrantzas
Publicado en: Macromolecules, 2020, ISSN 0024-9297
Editor: American Chemical Society
DOI: 10.1021/acs.macromol.0c00454

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

Autores: Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin, Li C Xue
Publicado en: Bioinformatics, Edición 36/1, 2019, Página(s) 112-121, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btz496

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

Autores: R. Vargas Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin.
Publicado en: Frontiers in Molecular Biosciences, Edición 8, 2021, ISSN 2296-889X
Editor: Frontiers Media S.A.
DOI: 10.3389/fmolb.2021.729513

Molecular Basis of CLC Antiporter Inhibition by Fluoride.

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

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

Autores: Matteo Aldeghi, Bert L. de Groot, Vytautas Gapsys
Publicado en: Computational Methods in Protein Evolution, Edición 1851, 2019, Página(s) 19-47, ISBN 978-1-4939-8735-1
Editor: Springer New York
DOI: 10.1007/978-1-4939-8736-8_2

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

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

Protein–Protein Modeling Using Cryo-EM Restraints

Autores: Mikael Trellet, Gydo van Zundert, Alexandre M. J. J. Bonvin
Publicado en: Structural Bioinformatics - Methods and Protocols, Edición 2112, 2020, Página(s) 145-162, ISBN 978-1-0716-0269-0
Editor: Springer US
DOI: 10.1007/978-1-0716-0270-6_11

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

Autores: F. Ambrosetti, Zuzana Jandova and A.M.J.J. Bonvin
Publicado en: 2020
Editor: arvix
DOI: 10.48550/arXiv.2005.03283

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

Autores: F. Ambrosetti, T.H. Olsed, P.P. Olimpieri, B. Jiménez-García, E. Milanetti, P. Marcatilli and A.M.J.J. Bonvin
Publicado en: bioRxiv, 2020, ISSN 0362-4331
Editor: 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'

Autores: V. Gapsys and B.L. de Groot
Publicado en: 2019, ISSN 2050-084X
Editor: eLife: Accelerating discovery
DOI: 10.7554/elife.44718.001

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