Centre of Excellence for Biomolecular Research

Rezultaty

This document will report on the status and outcome of the dissemination/outreach activities, and present plans about their execution in the second half of the project.

Long-term hardware/software assessment for pilot applications and the general community

A report discussing future hardware developments and their impact on the pilot applications; update to D1.3

Selection and Establishment of User Groups

A report detailing the selection of User Groups and how they were established including the provision of social media and other collaborative tools

Quality assurance and risk management plan.

This deliverable will discuss the overall quality monitoring process for the project (such as deliverables and milestone completion) and the overall risk management strategy. The risks will be regularly assessed in the yearly management report. The deliverable will also include the targets of the KPIs and success criteria, which will be followed-up in the management reports.

Revised business plan - update

A revision of D5.2 based on additional work with external consulting company.

Initial business plan.

An initial business plan based on the sketch in this proposal and initial experiences in WP3 will be developed.

Consultancy Modalities and Funding Options, Half-time Update

Yearly Update of the Consultancy Modalities and Funding Options

User feedback and future roadmap.

This deliverable will collect user feedback and identify future developments for the BioExcel supported environments.

Specification of software engineering, testing & QA

A report specifying the software engineering, testing, and quality assurance aspects of the project.

Roadmap of future hardware and long-term development plan for each pilot application.

A report discussing future hardware developments and their impact on the pilot applications.

Training report and updated plan

This document will report on the status of the generated training material, its usage and recommendation for its further improvements. The document will also contain evaluation of the completed training activities and recommendations for future ones.

Recommendations for BioExcel training programme.

This document will report on the outcome from the evaluation of the training needs and the plans for further training activities.

Dissemination and outreach plan

This document will outline the overall plan for dissemination and outreach activities.

Revised business plan.

A revision of D5.1 based on further experiences in WP3.

Final report on dissemination and training

This document will present a final report on the dissemination, outreach and training activities.

Consultancy Proposals Update

Update on the Consultancy Proposals

Efficacy of Feedback Process

A report on the efficacy of the feedback process. This deliverable will also cover the project’s agreed measures of success.

Governance and Business plan

A proposed governance structure with defined roles, responsibilities and internal communication processes will be developed together with the final revised business plan. This will also include proposals for a legal structure to be implemented for the CoE after the funding period is over. According to the recommendations at the 2nd EC review an external consultant, contracted under Article 10, will be used to validate the business plan.

State of the art and Gap analysis

This deliverable will report state of the art of portable environments for computing, will identify technological gaps based on the defined use cases and initial user feedback from WP3, and propose an initial roadmap.

Management plan

Initial deliverable stating the management organization and planning for the entire project.

Consultancy Proposals.

A report summarising the consultancy proposals developed by the BioExcel partners either for their benefit or for a collaborating organisation

Competency framework, mapping to current training & initial training plan

Working with our users, we will agree on the competencies that they require to make the most of HPC for their research and then match these competencies to those already provided by existing training programmes so that we can focus on developing new training that meets currently unmet needs.

Consultancy Modalities and Funding Options, Final Update

Final Update of Consultancy Modalities and Funding Options

Final release of workflows and modular tools for user services.

The final release will try to integrate user feedback provided in D2.3 and build a development plan for future developments.

First project release of all pilot applications

Public release of the pilot applications with documentation.

First release of workflows blocks and portals

The fist release of the customized environments as laid out in D2.1 will provide pilot users the opportunity to evaluate our platform and provide feedback.

Final project releases of pilot applications

Final public release of the pilot applications, including task-level parallelism and throughput modules, as well as a report of software achievements in the project and strategies for best usage of extreme-scale resources.

Publikacje

The Archive and Package (arcp) URI scheme

Autorzy: Stian Soiland-Reyes Marcos Cáceres
Opublikowane w: 2018 IEEE 14th International Conference on e-Science (e-Science), 2018, Strona(/y) 5, ISBN 978-1-5386-9156-4
Wydawca: IEEE
DOI: 10.1109/eScience.2018.0001

I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets

Autorzy: 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
Opublikowane w: 2016 IEEE International Conference on Big Data (Big Data), 2016, Strona(/y) 319-328, ISBN 978-1-4673-9005-7
Wydawca: IEEE
DOI: 10.1109/BigData.2016.7840618

Developing a Benchmark Suite for Semantic Web Data from Existing Workflows

Autorzy: Troumpoukis, Antonis; Charalambidis, Angelos; Mouchakis, Giannis; Konstantopoulos, Stasinos; Siebes, Ronald; de Boer, Victor; Soiland-Reyes, Stian; Digles, Daniela
Opublikowane w: Proceedings of the Workshop on Benchmarking Linked Data (BLINK 2016) co-located with the 15th International Semantic Web Conference (ISWC), Numer 1700, 2016, ISSN 1613-0073
Wydawca: CEUR-WS
DOI: 10.5281/zenodo.159568

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

Autorzy: 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
Opublikowane w: PLOS Biology, Numer 16/12, 2018, Strona(/y) e3000099, ISSN 1545-7885
Wydawca: PLOS
DOI: 10.1371/journal.pbio.3000099

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

Autorzy: 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
Opublikowane w: Data Science and Engineering, Numer 2/3, 2017, Strona(/y) 232-244, ISSN 2364-1185
Wydawca: Springer Nature Switzerland
DOI: 10.1007/s41019-017-0050-4

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

Autorzy: Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
Opublikowane w: Journal of Computer-Aided Molecular Design, Numer 33/1, 2019, Strona(/y) 83-91, ISSN 0920-654X
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10822-018-0148-4

Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server

Autorzy: Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin
Opublikowane w: Bioinformatics, 2018, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/bty816

A Membrane Protein Complex Docking Benchmark

Autorzy: Panagiotis I. Koukos, Inge Faro, Charlotte W. van Noort, Alexandre M.J.J. Bonvin
Opublikowane w: Journal of Molecular Biology, Numer 430/24, 2018, Strona(/y) 5246-5256, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2018.11.005

Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations

Autorzy: Tomas Bastys, Vytautas Gapsys, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina
Opublikowane w: Journal of Chemical Theory and Computation, Numer 14/7, 2018, Strona(/y) 3397-3408, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.7b01109

Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function

Autorzy: Viveca Lindahl, Pontus Gourdon, Magnus Andersson, Berk Hess
Opublikowane w: Scientific Reports, Numer 8/1, 2018, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-018-21357-2

Defining distance restraints in HADDOCK

Autorzy: Alexandre M. J. J. Bonvin, Ezgi Karaca, Panagiotis L. Kastritis, João P. G. L. M. Rodrigues
Opublikowane w: Nature Protocols, Numer 13/7, 2018, Strona(/y) 1503-1503, ISSN 1754-2189
Wydawca: Nature Publishing Group
DOI: 10.1038/s41596-018-0017-6

GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations

Autorzy: Rodolfo Briones, Christian Blau, Carsten Kutzner, Bert L. de Groot, Camilo Aponte-Santamaría
Opublikowane w: Biophysical Journal, Numer 116/1, 2019, Strona(/y) 4-11, ISSN 0006-3495
Wydawca: Biophysical Society
DOI: 10.1016/j.bpj.2018.11.3126

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

Autorzy: Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin
Opublikowane w: Proteins: Structure, Function, and Bioinformatics, Numer 87/2, 2019, Strona(/y) 110-119, ISSN 0887-3585
Wydawca: Wiley-Liss Inc
DOI: 10.1002/prot.25630

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

Autorzy: 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
Opublikowane w: Journal of Computer-Aided Molecular Design, Numer 32/1, 2018, Strona(/y) 175-185, ISSN 0920-654X
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10822-017-0049-y

Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification

Autorzy: Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone
Opublikowane w: BMC Bioinformatics, Numer 19/S15, 2018, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-018-2414-9

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots

Autorzy: 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
Opublikowane w: Scientific Reports, Numer 7/1, 2017, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-017-08321-2

M3: an integrative framework for structure determination of molecular machines

Autorzy: Ezgi Karaca, João P G L M Rodrigues, Andrea Graziadei, Alexandre M J J Bonvin, Teresa Carlomagno
Opublikowane w: Nature Methods, Numer 14/9, 2017, Strona(/y) 897-902, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/nmeth.4392

Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution

Autorzy: Anna Rubio-Cosials, Federica Battistini, Alexander Gansen, Anna Cuppari, Pau Bernadó, Modesto Orozco, Jörg Langowski, Katalin Tóth, Maria Solà
Opublikowane w: Biophysical Journal, Numer 114/10, 2018, Strona(/y) 2386-2396, ISSN 0006-3495
Wydawca: Biophysical Society
DOI: 10.1016/j.bpj.2017.11.3743

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes

Autorzy: Vytautas Gapsys, Bert L. de Groot
Opublikowane w: Journal of Chemical Theory and Computation, Numer 13/12, 2017, Strona(/y) 6275-6289, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.7b00849

Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes

Autorzy: 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 Sca
Opublikowane w: Nature Communications, Numer 9/1, 2018, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-018-04110-1

The Differential Response of Proteins to Macromolecular Crowding

Autorzy: Michela Candotti, Modesto Orozco
Opublikowane w: PLOS Computational Biology, Numer 12/7, 2016, Strona(/y) e1005040, ISSN 1553-7358
Wydawca: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1005040

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

Autorzy: Víctor López-Ferrando, Andrea Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Ll Gelpí
Opublikowane w: Nucleic Acids Research, 2017, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkx313

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

Autorzy: Laura Orellana, Ozge Yoluk, Oliver Carrillo, Modesto Orozco, Erik Lindahl
Opublikowane w: Nature Communications, Numer 7, 2016, Strona(/y) 12575, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/ncomms12575

Long-timescale dynamics of the Drew?Dickerson dodecamer

Autorzy: Pablo D. Dans, Linda Danil?ne, Ivan Ivani, Tom?? Dr?ata, Filip Lanka?, Adam Hospital, J?rgen Walther, Ricard Illa Pujagut, Federica Battistini, Josep Lluis Gelp?, Richard Lavery, Modesto Orozco
Opublikowane w: Nucleic Acids Research, Numer 44/9, 2016, Strona(/y) 4052-4066, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkw264

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

Autorzy: Ardita Shkurti, Ramon Goni, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles A. Laughton
Opublikowane w: SoftwareX, Numer 5, 2016, Strona(/y) 44-50, ISSN 2352-7110
Wydawca: Elsevier B.V.
DOI: 10.1016/j.softx.2016.04.002

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

Autorzy: Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpí
Opublikowane w: Nucleic Acids Research, Numer 44/D1, 2016, Strona(/y) D272-D278, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkv1301

Parmbsc1: a refined force field for DNA simulations

Autorzy: Ivan Ivani, Pablo D Dans, Agnes Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluis Gelpí, Carlos González, Michele Vendruscolo, Charles A Laughton, Sarah A Harris, David A Case, Modesto Orozco
Opublikowane w: Nature Methods, 2015, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/nmeth.3658

Proton Dynamics in Protein Mass Spectrometry

Autorzy: Jinyu Li, Wenping Lyu, Giulia Rossetti, Albert Konijnenberg, Antonino Natalello, Emiliano Ippoliti, Modesto Orozco, Frank Sobott, Rita Grandori, Paolo Carloni
Opublikowane w: The Journal of Physical Chemistry Letters, Numer 8/6, 2017, Strona(/y) 1105-1112, ISSN 1948-7185
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpclett.7b00127

Environmental and genetic factors support the dissociation between ?-synuclein aggregation and toxicity

Autorzy: Anna Villar-Piqu?, Tom?s Lopes da Fonseca, Ricardo Sant?Anna, ?va M?nika Szeg?, Luis Fonseca-Ornelas, Raquel Pinho, Anita Carija, Ellen Gerhardt, Caterina Masaracchia, Enrique Abad Gonzalez, Giulia Rossetti, Paolo Carloni, Claudio O. Fern?ndez, Debora Foguel, Ira Milosevic, Markus Zweckstetter, Salvador Ventura, Tiago Fleming Outeiro
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 113/42, 2016, Strona(/y) E6506-E6515, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1606791113

Challenges of docking in large, flexible and promiscuous binding sites

Autorzy: Martin Kotev, Robert Soliva, Modesto Orozco
Opublikowane w: Bioorganic & Medicinal Chemistry, Numer 24/20, 2016, Strona(/y) 4961-4969, ISSN 0968-0896
Wydawca: Pergamon Press Ltd.
DOI: 10.1016/j.bmc.2016.08.010

dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking

Autorzy: Dimitrios Spiliotopoulos, Panagiotis L. Kastritis, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri
Opublikowane w: Frontiers in Molecular Biosciences, Numer 3, 2016, ISSN 2296-889X
Wydawca: Frontiers
DOI: 10.3389/fmolb.2016.00046

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

Autorzy: 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
Opublikowane w: Journal of Molecular Biology, Numer 428/4, 2016, Strona(/y) 720-725, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2015.09.014

Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students

Autorzy: João P.G.L.M. Rodrigues, Adrien S.J. Melquiond, Alexandre M.J.J. Bonvin
Opublikowane w: Biochemistry and Molecular Biology Education, Numer 44/2, 2016, Strona(/y) 160-167, ISSN 1470-8175
Wydawca: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1002/bmb.20941

The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes

Autorzy: G.C.P. van Zundert, M. Trellet, J. Schaarschmidt, Z. Kurkcuoglu, M. David, M. Verlato, A. Rosato, A.M.J.J. Bonvin
Opublikowane w: Journal of Molecular Biology, Numer 429/3, 2017, Strona(/y) 399-407, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2016.11.032

Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes

Autorzy: Cunliang Geng, Anna Vangone, Alexandre M.J.J. Bonvin
Opublikowane w: Protein Engineering Design and Selection, Numer 29/8, 2016, Strona(/y) 291-299, ISSN 1741-0126
Wydawca: Oxford University Press
DOI: 10.1093/protein/gzw020

Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling

Autorzy: Iman Pouya, Sander Pronk, Magnus Lundborg, Erik Lindahl
Opublikowane w: Future Generation Computer Systems, Numer 71, 2017, Strona(/y) 18-31, ISSN 0167-739X
Wydawca: Elsevier BV
DOI: 10.1016/j.future.2016.11.004

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

Autorzy: Dari Kimanius, Björn O Forsberg, Sjors HW Scheres, Erik Lindahl
Opublikowane w: eLife, Numer 5, 2016, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/eLife.18722

Changes in the free-energy landscape of p38? MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

Autorzy: Antonija Kuzmanic, Ludovico Sutto, Giorgio Saladino, Angel R Nebreda, Francesco L Gervasio, Modesto Orozco
Opublikowane w: eLife, Numer 6, 2017, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/eLife.22175

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan

Autorzy: Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de?Groot
Opublikowane w: Angewandte Chemie International Edition, Numer 55/26, 2016, Strona(/y) 7364-7368, ISSN 1433-7851
Wydawca: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201510054

Multiscale simulation of DNA

Autorzy: Pablo D Dans, J?rgen Walther, Hansel G?mez, Modesto Orozco
Opublikowane w: Current Opinion in Structural Biology, Numer 37, 2016, Strona(/y) 29-45, ISSN 0959-440X
Wydawca: Elsevier BV
DOI: 10.1016/j.sbi.2015.11.011

Structure of the bacterial plant-ferredoxin receptor FusA

Autorzy: 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
Opublikowane w: Nature Communications, Numer 7, 2016, Strona(/y) 13308, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/ncomms13308

pmx Webserver: A User Friendly Interface for Alchemistry

Autorzy: Vytautas Gapsys, Bert L. de Groot
Opublikowane w: Journal of Chemical Information and Modeling, Numer 57/2, 2017, Strona(/y) 109-114, ISSN 1549-9596
Wydawca: American Chemical Society
DOI: 10.1021/acs.jcim.6b00498

The Multiple Roles of Waters in Protein Solvation

Autorzy: Adam Hospital, Michela Candotti, Josep Llu?s Gelp?, Modesto Orozco
Opublikowane w: The Journal of Physical Chemistry B, Numer 121/15, 2017, Strona(/y) 3636-3643, ISSN 1520-6106
Wydawca: American Chemical Society
DOI: 10.1021/acs.jpcb.6b09676

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance

Autorzy: Radoslaw Pluta, D. Roeland Boer, Fabián Lorenzo-Díaz, Silvia Russi, Hansel Gómez, Cris Fernández-López, Rosa Pérez-Luque, Modesto Orozco, Manuel Espinosa, Miquel Coll
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 114/32, 2017, Strona(/y) E6526-E6535, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1702971114

BioExcel Whitepaper on Scientific Software Development

Autorzy: Abraham, Mark J.; Melquiond, Adrien S.J.; Ippoliti, Emiliano; Gapsys, Vytautas; Hess, Berk; Trellet, Mikael; Rodrigues, João P.G.L.M.; Laure, Erwin; Apostolov, Rossen; de Groot, Bert L.; Bonvin, Alexandre M.J.J.; Lindahl, Erik
Opublikowane w: Numer 3, 2018
Wydawca: openAIRE
DOI: 10.5281/zenodo.1194633

BioExcel Deliverable 3.4 - Efficacy of Feedback Processes

Autorzy: Carter, Adam; Harrow, Ian; Abraham, Mark; Hospital, Adam; Matser, Vera; Noack, Holger; Apostolov, Rossen
Opublikowane w: Numer 3, 2017
Wydawca: BioExcel
DOI: 10.5281/zenodo.1060843

BioExcel Deliverable 1.2 – First project release of all pilot applications

Autorzy: Abraham, Mark; Ippoliti, Emiliano; Bonvin, Alexandre; de Groot, Bert; Soiland-Reyes, Stian
Opublikowane w: Numer 6, 2017
Wydawca: BioExcel
DOI: 10.5281/zenodo.574459

BioExcel Deliverable 4.1 – Dissemination and Outreach Plan

Autorzy: Apostolov, Rossen
Opublikowane w: Numer 37, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.264250

BioExcel Deliverable 4.2 - Competency framework, mapping to current training & initial training plan

Autorzy: Matser, Vera
Opublikowane w: Numer 31, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.264231

BioExcel Deliverable 2.1 – State of the art and gap analysis

Autorzy: Hospital, Adam; Montras, Anna; Soiland-Reyes, Stian; Bonvin, Alexandre; Melquiond, Adrien; Gelpí, Josep Lluís; Lezzi, Daniele; Newhouse, Steven; Dianes, Jose A.; Abraham, Mark; Apostolov, Rossen; Ippoliti, Emiliano; Carter, Adam; White, Darren J.
Opublikowane w: Numer 35, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.263963

BioExcel Deliverable 3.1 - Selection and Establishment of User Groups

Autorzy: Carter, Adam; Harrow, Ian; Apostolov, Rossen; Soiland-Reyes, Stian; de Groot, Bert; Abraham, Mark
Opublikowane w: Numer 36, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.264011

BioExcel Deliverable 3.3 – Consultancy Modalities and Funding Options, Half-time Update

Autorzy: Carter, Adam; Harrow, Ian
Opublikowane w: Numer 6, 2017
Wydawca: BioExcel
DOI: 10.5281/zenodo.574613

BioExcel Deliverable 5.1 - Initial Business Plan

Autorzy: Noack, Holger; Harrow, Ian; Bonvin, Alexandre; Carter, Adam; Apostolov, Rossen; Laure, Erwin
Opublikowane w: Numer 28, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.263932

BioExcel Deliverable 6.2 – Quality Assurance and Risk Management Plan

Autorzy: Apostolov, Rossen
Opublikowane w: Numer 25, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.263934

BioExcel Deliverable 6.1 - Management Plan

Autorzy: Apostolov, Rossen; Laure, Erwin
Opublikowane w: Numer 26, 2015
Wydawca: BioExcel
DOI: 10.5281/zenodo.263933

BioExcel Deliverable 2.2 – First Release of Workflow Blocks and Portals

Autorzy: Hospital, Adam; Montras, Anna; Gelpí, Josep Lluís; Badia, Rosa M.; Newhouse, Steven; Dianes, Jose A.; Andrio, Pau; Soiland-Reyes, Stian; White, Darren J; Carter, Adam; Ippoliti, Emiliano; Melquiond, Adrien; de Groot, Bert
Opublikowane w: Numer 16, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.263965

BioExcel Deliverable 1.1 - Specification of software engineering, testing & QA

Autorzy: Abraham, Mark; Bonvin, Alexandre; Melquiond, Adrien; Ippoliti, Emiliano; de Groot, Bert
Opublikowane w: Numer 17, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.263908

BioExcel Deliverable 4.3 - Recommendations for BioExcel Training Programme

Autorzy: Matser, Vera
Opublikowane w: Numer 18, 2016
Wydawca: BioExcel
DOI: 10.5281/zenodo.263926

BioExcel Deliverable 3.2 – Consultancy Proposals

Autorzy: Carter, Adam
Opublikowane w: Numer 9, 2017
Wydawca: BioExcel
DOI: 10.5281/zenodo.574607

BioExcel Deliverable 1.3 - Roadmap of future hardware and long-term development plan for each pilot application

Autorzy: Apostolov, Rossen; Abraham, Mark; Laure, Erwin; Lindahl, Erik; Bonvin, Alexandre; de Groot, Bert; Ippoliti, Emiliano
Opublikowane w: Numer 6, 2017
Wydawca: BioExcel
DOI: 10.5281/zenodo.574605

BioExcel Deliverable 5.2 - Revised Business Plan

Autorzy: Noack, Holger; Harrow, Ian; Bonvin, Alexandre; Carter, Adam; Apostolov, Rossen; Laure, Erwin
Opublikowane w: Numer 6, 2017
Wydawca: BioExcel
DOI: 10.5281/zenodo.574634

BioExcel Deliverable 4.5 – Training report and updated plan

Autorzy: Matser, Vera
Opublikowane w: Numer 6, 2017
Wydawca: BioExcel
DOI: 10.5281/zenodo.574620

GROMACS 2019.1 Manual

Autorzy: Lindahl; Abraham; Hess; van der Spoel
Opublikowane w: Numer 25, 2018
Wydawca: BioExcel
DOI: 10.5281/zenodo.2564761

GROMACS 2019 Manual

Autorzy: Lindahl; Abraham; Hess; van der Spoel
Opublikowane w: Numer 1, 2018
Wydawca: BioExcel
DOI: 10.5281/zenodo.2424485

Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop

Autorzy: Eva S. Cunha, Pedro Sfriso, Adriana L. Rojas, Pietro Roversi, Adam Hospital, Modesto Orozco, Nicola G.A. Abrescia
Opublikowane w: Structure, Numer 25/1, 2017, Strona(/y) 53-65
Wydawca: Cell Press
DOI: 10.1016/j.str.2016.11.003

BioExcel Deliverable 4.4 – Dissemination Report and Updated Plan

Autorzy: Apostolov, Rossen; Matser, Vera; White, Mirren; Harrow, Ian
Opublikowane w: Numer 1, 2017
Wydawca: BioExcel
DOI: 10.5281/zenodo.574614

BioExcel Deliverable 2.3 - User Feedback and Future Roadmap

Autorzy: Hospital, Adam; Gelpí, Josep Lluís; Dianes, Jose A.; Andrio, Pau; White, Darren J.; Ippoliti, Emiliano; Melquiond, Adrien; Gapsys, Vytautas
Opublikowane w: Zenodo, Numer 3, 2017, ISSN 0000-0000
Wydawca: BioExcel
DOI: 10.5281/zenodo.1060946

Software release for BioExcel pilot applications

Autorzy: Mark Abraham
Opublikowane w: Zenodo, Numer 2, 2018, ISSN 0000-0000
Wydawca: BioExcel
DOI: 10.5281/zenodo.1473684

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