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BioExcel Centre of Excellence for ComputationalBiomolecular Research

Deliverables

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.

Business Model design report

Detailed BioExcel Business Model for taking the project into a sustainability phase

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

Annotated and justified Service Catalogue

A first list of exploitable assets identified

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.

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

Publications

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

Author(s): Montserrat Terrazas, Vito Genna, Guillem Portella, Núria Villegas, Dani Sánchez, Carme Arnan, Carlos Pulido-Quetglas, Rory Johnson, Roderic Guigó, Isabelle Brun-Heath, Anna Aviñó, Ramon Eritja, Modesto Orozco
Published in: Chem, Issue 5/6, 2019, Page(s) 1619-1631, ISSN 2451-9294
DOI: 10.1016/j.chempr.2019.04.002

A molecular mechanism for transthyretin amyloidogenesis

Author(s): Ai Woon Yee, Matteo Aldeghi, Matthew P. Blakeley, Andreas Ostermann, Philippe J. Mas, Martine Moulin, Daniele de Sanctis, Matthew W. Bowler, Christoph Mueller-Dieckmann, Edward P. Mitchell, Michael Haertlein, Bert L. de Groot, Elisabetta Boeri Erba, V. Trevor Forsyth
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-08609-z

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

Author(s): Richard A Norman, Francesco Ambrosetti, Alexandre M J J Bonvin, Lucy J Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk
Published in: Briefings in Bioinformatics, 2019, ISSN 1467-5463
DOI: 10.1093/bib/bbz095

LightDock goes information-driven

Author(s): Jorge Roel-Touris, Alexandre M J J Bonvin, Brian Jiménez-García
Published in: Bioinformatics, Issue 36/3, 2019, Page(s) 950-952, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz642

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

Author(s): Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
Published in: Journal of Computer-Aided Molecular Design, Issue 33/1, 2019, Page(s) 83-91, ISSN 0920-654X
DOI: 10.1007/s10822-018-0148-4

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

Author(s): Panagiotis I. Koukos, Jorge Roel‐Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E. Trellet, Adrien S. J. Melquiond, Li C. Xue, Rodrigo V. Honorato, Irina Moreira, Zeynep Kurkcuoglu, Anna Vangone, Alexandre M. J. J. Bonvin
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 88/8, 2020, Page(s) 1029-1036, ISSN 0887-3585
DOI: 10.1002/prot.25869

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

Author(s): Alexandra Balaceanu, Diana Buitrago, Jürgen Walther, Adam Hospital, Pablo D Dans, Modesto Orozco
Published in: Nucleic Acids Research, Issue 47/9, 2019, Page(s) 4418-4430, ISSN 0305-1048
DOI: 10.1093/nar/gkz255

Molywood: streamlining the design and rendering of molecular movies

Author(s): Miłosz Wieczór, Adam Hospital, Genis Bayarri, Jacek Czub, Modesto Orozco
Published in: Bioinformatics, 2020, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btaa584

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

Author(s): H.M. Berman, P,D. Adams, A.M.J.J. Bonvin, S.K. Burley, B. Carragher, W. Chiu, F. DiMaio, T.E. Ferrin, M.J. Gabanyi, T.D. Goddard, P.R. Griffin, J. Haas, C.A. Hanke, J.C. Hoch, G. Hummer, G. Kurisu, C.L. Lawson, A. Leitner, J.L. Markley, J. Meiler, G.T. Montelione, G.N. Phillips Jr., T. Prisner, J. Rappsilber, D.C. Schriemer, T. Schwede, C.A.M. Seidel, T.S. Strutzenberg, D.I. Svergun, E. Tajkhorshi
Published in: Structure, Issue 27/12, 2019, Page(s) 1745-1759, ISSN 2352-0124
DOI: 10.1016/j.str.2019.11.002

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

Author(s): Antonija Kuzmanic, Pablo D. Dans, Modesto Orozco
Published in: Chem, Issue 5/3, 2019, Page(s) 649-663, ISSN 2451-9294
DOI: 10.1016/j.chempr.2018.12.007

A multifunctional toolkit for target-directed cancer therapy

Author(s): Montserrat Terrazas, Dani Sánchez, Federica Battistini, Núria Villegas, Isabelle Brun-Heath, Modesto Orozco
Published in: Chemical Communications, Issue 55/6, 2019, Page(s) 802-805, ISSN 1359-7345
DOI: 10.1039/c8cc08823c

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

Author(s): Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 87/2, 2019, Page(s) 110-119, ISSN 0887-3585
DOI: 10.1002/prot.25630

Natural helix 9 mutants of PPARγ differently affect its transcriptional activity

Author(s): Marjoleine F. Broekema, Maarten P.G. Massink, Cinzia Donato, Joep de Ligt, Joerg Schaarschmidt, Anouska Borgman, Marieke G. Schooneman, Diana Melchers, Martin N. Gerding, René Houtman, Alexandre M.J.J. Bonvin, Amit R. Majithia, Houshang Monajemi, Gijs W. van Haaften, Maarten R. Soeters, Eric Kalkhoven
Published in: Molecular Metabolism, Issue 20, 2019, Page(s) 115-127, ISSN 2212-8778
DOI: 10.1016/j.molmet.2018.12.005

DNA specificities modulate the binding of human transcription factor A to mitochondrial DNA control region

Author(s): Anna Cuppari, Pablo Fernández-Millán, Federica Battistini, Aleix Tarrés-Solé, Sébastien Lyonnais, Guillermo Iruela, Elena Ruiz-López, Yuliana Enciso, Anna Rubio-Cosials, Rafel Prohens, Miquel Pons, Carlos Alfonso, Katalin Tóth, Germán Rivas, Modesto Orozco, Maria Solà
Published in: Nucleic Acids Research, Issue 47/12, 2019, Page(s) 6519-6537, ISSN 0305-1048
DOI: 10.1093/nar/gkz406

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

Author(s): Pablo D. Dans, Diego Gallego, Alexandra Balaceanu, Leonardo Darré, Hansel Gómez, Modesto Orozco
Published in: Chem, Issue 5/1, 2019, Page(s) 51-73, ISSN 2451-9294
DOI: 10.1016/j.chempr.2018.09.015

Integrative Modelling of Biomolecular Complexes

Author(s): P.I. Koukos, A.M.J.J. Bonvin
Published in: Journal of Molecular Biology, Issue 432/9, 2020, Page(s) 2861-2881, ISSN 0022-2836
DOI: 10.1016/j.jmb.2019.11.009

Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

Author(s): Leander Goldbach, Bram J. A. Vermeulen, Sami Caner, Minglong Liu, Christina Tysoe, Lieke van Gijzel, Ryoji Yoshisada, Mikael Trellet, Hugo van Ingen, Gary D. Brayer, Alexandre M. J. J. Bonvin, Seino A. K. Jongkees
Published in: ACS Chemical Biology, Issue 14/8, 2019, Page(s) 1751-1759, ISSN 1554-8929
DOI: 10.1021/acschembio.9b00290

Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype–phenotype correlation

Author(s): Emanuele G. Coci, Vytautas Gapsys, Natasha Shur, Yoon Shin‐Podskarbi, Bert L. Groot, Kathryn Miller, Jerry Vockley, Neal Sondheimer, Rebecca Ganetzky, Peter Freisinger
Published in: Human Mutation, Issue 40/6, 2019, Page(s) 816-827, ISSN 1059-7794
DOI: 10.1002/humu.23742

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

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

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

Author(s): Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, Alexandre M.J.J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock, Manuela Helmer-Citterich, Adam Hospital, Modesto Orozco, Anastassis Perrakis, Matthias Rarey, Claudio Soares, Joel L. Sussman, Janet M. Thornton, Pierre Tuffery, Gabor Tusnady, Rikkert Wierenga, Tiina Salminen, Bohdan S
Published in: F1000Research, Issue 9, 2020, Page(s) 278, ISSN 2046-1402
DOI: 10.12688/f1000research.20559.1

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

Author(s): Matteo Aldeghi, Vytautas Gapsys, Bert L. de Groot
Published in: ACS Central Science, Issue 5/8, 2019, Page(s) 1468-1474, ISSN 2374-7943
DOI: 10.1021/acscentsci.9b00590

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition

Author(s): Federica Battistini, Adam Hospital, Diana Buitrago, Diego Gallego, Pablo D. Dans, Josep Lluis Gelpí, Modesto Orozco
Published in: Journal of Molecular Biology, Issue 431/19, 2019, Page(s) 3845-3859, ISSN 0022-2836
DOI: 10.1016/j.jmb.2019.07.021

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

Author(s): Elin Claesson, Weixiao Yuan Wahlgren, Heikki Takala, Suraj Pandey, Leticia Castillon, Valentyna Kuznetsova, Léocadie Henry, Matthijs Panman, Melissa Carrillo, Joachim Kübel, Rahul Nanekar, Linnéa Isaksson, Amke Nimmrich, Andrea Cellini, Dmitry Morozov, Michał Maj, Moona Kurttila, Robert Bosman, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, So Iwata, Shigeki Owada, Keith Moffat, Gerrit
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
DOI: 10.7554/elife.53514

Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4

Author(s): Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Published in: Journal of Computer-Aided Molecular Design, Issue 34/2, 2020, Page(s) 149-162, ISSN 0920-654X
DOI: 10.1007/s10822-019-00244-6

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

Author(s): Pablo D Dans, Alexandra Balaceanu, Marco Pasi, Alessandro S Patelli, Daiva Petkevičiūtė, Jürgen Walther, Adam Hospital, Genís Bayarri, Richard Lavery, John H Maddocks, Modesto Orozco
Published in: Nucleic Acids Research, Issue 47/21, 2019, Page(s) 11090-11102, ISSN 0305-1048
DOI: 10.1093/nar/gkz905

Surviving the deluge of biosimulation data

Author(s): Adam Hospital, Federica Battistini, Robert Soliva, Josep Lluis Gelpí, Modesto Orozco
Published in: WIREs Computational Molecular Science, Issue 10/3, 2020, ISSN 1759-0876
DOI: 10.1002/wcms.1449

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

Author(s): Marc F. Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil, Tereza Gerguri, Paul A. Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran‐Ran Liu, Xi‐Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov,
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 87/12, 2019, Page(s) 1200-1221, ISSN 0887-3585
DOI: 10.1002/prot.25838

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset

Author(s): Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga
Published in: Journal of Computer-Aided Molecular Design, Issue 33/12, 2019, Page(s) 1031-1043, ISSN 0920-654X
DOI: 10.1007/s10822-019-00232-w

Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond Is Locked

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

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

Author(s): Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Published in: Journal of Chemical Information and Modeling, Issue 59/4, 2019, Page(s) 1515-1528, ISSN 1549-9596
DOI: 10.1021/acs.jcim.8b00730

Mode of action of teixobactins in cellular membranes

Author(s): Rhythm Shukla, João Medeiros-Silva, Anish Parmar, Bram J. A. Vermeulen, Sanjit Das, Alessandra Lucini Paioni, Shehrazade Jekhmane, Joseph Lorent, Alexandre M. J. J. Bonvin, Marc Baldus, Moreno Lelli, Edwin J. A. Veldhuizen, Eefjan Breukink, Ishwar Singh, Markus Weingarth
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-020-16600-2

EXPLORING THE CONFORMATIONAL LANDSCAPE OF BIOACTIVE SMALL MOLECULES

Author(s): Sanja Zivanovic, Francesco Colizzi, David Moreno, Adam Hospital, Robert Soliva, Modesto Orozco
Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
DOI: 10.1021/acs.jctc.0c00304

Finding the ΔΔ G spot: Are predictors of binding affinity changes upon mutations in protein-protein interactions ready for it?

Author(s): Cunliang Geng, Li C. Xue, Jorge Roel-Touris, Alexandre M. J. J. Bonvin
Published in: Wiley Interdisciplinary Reviews: Computational Molecular Science, Issue 9/5, 2019, Page(s) e1410, ISSN 1759-0876
DOI: 10.1002/wcms.1410

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

Author(s): Juan Aranda, Montserrat Terrazas, Hansel Gómez, Núria Villegas, Modesto Orozco
Published in: Nature Catalysis, Issue 2/6, 2019, Page(s) 544-552, ISSN 2520-1158
DOI: 10.1038/s41929-019-0290-y

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

Author(s): Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera
Published in: Journal of Computer-Aided Molecular Design, Issue 34/5, 2020, Page(s) 601-633, ISSN 0920-654X
DOI: 10.1007/s10822-020-00290-5

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

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

Molecular Basis of CLC Antiporter Inhibition by Fluoride

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

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

Author(s): Albert Escobedo, Busra Topal, Micha B. A. Kunze, Juan Aranda, Giulio Chiesa, Daniele Mungianu, Ganeko Bernardo-Seisdedos, Bahareh Eftekharzadeh, Margarida Gairí, Roberta Pierattelli, Isabella C. Felli, Tammo Diercks, Oscar Millet, Jesús García, Modesto Orozco, Ramon Crehuet, Kresten Lindorff-Larsen, Xavier Salvatella
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-09923-2

West-Life: A Virtual Research Environment for structural biology

Author(s): Chris Morris, Paolo Andreetto, Lucia Banci, Alexandre M.J.J. Bonvin, Grzegorz Chojnowski, Laura del Cano, José Marıa Carazo, Pablo Conesa, Susan Daenke, George Damaskos, Andrea Giachetti, Natalie E.C. Haley, Maarten L. Hekkelman, Philipp Heuser, Robbie P. Joosten, Daniel Kouřil, Aleš Křenek, Tomáš Kulhánek, Victor S. Lamzin, Nurul Nadzirin, Anastassis Perrakis, Antonio Rosato, Fiona Sander
Published in: Journal of Structural Biology: X, Issue 1, 2019, Page(s) 100006, ISSN 2590-1524
DOI: 10.1016/j.yjsbx.2019.100006

BIOACTIVE CONFORMATIONAL ENSEMBLE SERVER AND DATABASE. A PUBLIC FRAMEWORK TO SPEED UP IN SILICO DRUG DISCOVERY

Author(s): Sanja Zivanovic, Genís Bayarri, Francesco Colizzi, David Moreno, Josep Lluis Gelpi, Robert Soliva, Adam Hospital, Modesto Orozco
Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
DOI: 10.1021/acs.jctc.0c00305

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

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

VeriNA3d: an R package for nucleic acids data mining

Author(s): Diego Gallego, Leonardo Darré, Pablo D Dans, Modesto Orozco
Published in: Bioinformatics, Issue 35/24, 2019, Page(s) 5334-5336, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz553

Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics

Author(s): Francesco Colizzi, Adam Hospital, Sanja Zivanovic, Modesto Orozco
Published in: Angewandte Chemie International Edition, Issue 58/12, 2019, Page(s) 3759-3763, ISSN 1433-7851
DOI: 10.1002/anie.201810922

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

Author(s): Tomas Bastys, Vytautas Gapsys, Hauke Walter, Eva Heger, Nadezhda T. Doncheva, Rolf Kaiser, Bert L. de Groot, Olga V. Kalinina
Published in: Retrovirology, Issue 17/1, 2020, ISSN 1742-4690
DOI: 10.1186/s12977-020-00520-6

Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems

Author(s): Zeynep Kurkcuoglu, Alexandre M. J. J. Bonvin
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 88/2, 2019, Page(s) 292-306, ISSN 0887-3585
DOI: 10.1002/prot.25802

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

Author(s): Anna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, Cunliang Geng, Nevia Citro, Mikael E Trellet, Li C Xue, Alexandre M J J Bonvin
Published in: Bioinformatics, Issue 35/9, 2018, Page(s) 1585-1587, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty816

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

Author(s): David Moreno, Sanja Zivanovic, Francesco Colizzi, Adam Hospital, Juan Aranda, Robert Soliva, Modesto Orozco
Published in: Journal of Chemical Theory and Computation, 2020, ISSN 1549-9618
DOI: 10.1021/acs.jctc.0c00306

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

Author(s): Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Published in: Chemical Science, Issue 11/4, 2020, Page(s) 1140-1152, ISSN 2041-6520
DOI: 10.1039/c9sc03754c

Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope

Author(s): Laura Orellana, Amy H. Thorne, Rafael Lema, Johan Gustavsson, Alison D. Parisian, Adam Hospital, Tiago N. Cordeiro, Pau Bernadó, Andrew M. Scott, Isabelle Brun-Heath, Erik Lindahl, Webster K. Cavenee, Frank B. Furnari, Modesto Orozco
Published in: Proceedings of the National Academy of Sciences, Issue 116/20, 2019, Page(s) 10009-10018, ISSN 0027-8424
DOI: 10.1073/pnas.1821442116

MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

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

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

Author(s): Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone
Published in: Bioinformatics, Issue 35/22, 2019, Page(s) 4821-4823, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz437

Molecular Dynamics Simulation of Amorphous Poly(3-hexylthiophene)

Author(s): Flora D. Tsourtou, Loukas D. Peristeras, Rossen Apostolov, Vlasis G. Mavrantzas
Published in: Macromolecules, 2020, ISSN 0024-9297
DOI: 10.1021/acs.macromol.0c00454

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

Author(s): Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M J J Bonvin, Li C Xue
Published in: Bioinformatics, Issue 36/1, 2019, Page(s) 112-121, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz496

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation

Author(s): Matteo Aldeghi, Bert L. de Groot, Vytautas Gapsys
Published in: Computational Methods in Protein Evolution, Issue 1851, 2019, Page(s) 19-47
DOI: 10.1007/978-1-4939-8736-8_2

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

Author(s): Jorge Ejarque, Marta Bertran, Javier Álvarez Cid-Fuentes, Javier Conejero, Rosa M. Badia
Published in: Euro-Par 2020: Parallel Processing - 26th International Conference on Parallel and Distributed Computing, Warsaw, Poland, August 24–28, 2020, Proceedings, Issue 12247, 2020, Page(s) 411-425
DOI: 10.1007/978-3-030-57675-2_26

Protein–Protein Modeling Using Cryo-EM Restraints

Author(s): Mikael Trellet, Gydo van Zundert, Alexandre M. J. J. Bonvin
Published in: Structural Bioinformatics - Methods and Protocols, Issue 2112, 2020, Page(s) 145-162
DOI: 10.1007/978-1-0716-0270-6_11

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

Author(s): F. Ambrosetti, T.H. Olsed, P.P. Olimpieri, B. Jiménez-García, E. Milanetti, P. Marcatilli and A.M.J.J. Bonvin
Published in: bioRxiv, 2020, ISSN 0362-4331
DOI: 10.1101/2020.03.18.967828

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

Author(s): V. Gapsys and B.L. de Groot
Published in: 2019, ISSN 2050-084X
DOI: 10.7554/elife.44718.001

Datasets

CWL run of RNA-seq Analysis Workflow (CWLProv 0.5.0 Research Object)

Author(s): Soiland-Reyes, Stian
Published in: Mendeley

HADDOCK file I/O benchmark

Author(s): Honorato, Rodrigo; Bonvin, Alexandre
Published in: Zenodo

D1.4 release of BioExcel QM/MM Benchmark Suite

Author(s): Proeme, Arno; Judge, Holly; Prat, Salome Llabres; Morovoz, Dmitry; Modi Vaibhav; Ippoliti, Emiliano
Published in: Zenodo

Cwlprov: Interoperable Retrospective Provenance Capture And Computational Analysis Sharing

Author(s): Farah Zaib Khan; Stian Soiland-Reyes; Richard O. Sinnott; Andrew Lonie; Carole Goble; Michael R. Crusoe

Docking models for Docking Benchmark 4, 5 and CAPRI score_set

Author(s): Bonvin, Alexandre; Geng, Cunliang; Xue, Li C..
Published in: SBGrid Data Bank

HADDOCK MD-scoring trajectories

Author(s): Jandova, Zuzana; Vargiu, Attilio Vittorio; Bonvin, Alexandre M.J.J.
Published in: Zenodo

HADDOCK Coarse-Grained Protein-DNA Docking Dataset

Author(s): Rodrigo V Honorato; Jorge Roel-Touris; Alexandre AMJJ Bonvin
Published in: Zenodo

ClustENM-HADDOCK pipeline models

Author(s): Bonvin, Alexandre; Kurkcuoglu, Zeynep
Published in: SBGrid Data Bank

Docking models of antibody-antigen complexes

Author(s): Ambrosetti, Francesco; Bonvin, Alexandre MJJ.; Jimenez-Garcia, Brian; Roel-Touris, Jorge
Published in: SBGrid Data Bank

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Author(s): Khan, Farah Zaib; Soiland-Reyes, Stian; Sinnott, Richard O.; Lonie, Andrew; Goble, Carole; Crusoe, Michael R.
Published in: Zenodo

HADDOCK models of mutant protein complexes

Author(s): Geng, Cunliang
Published in: SBGrid Data Bank

CWL run of Alignment Workflow (CWLProv 0.6.0 Research Object)

Author(s): Soiland-Reyes, Stian
Published in: Mendeley

Zenodo metadata JSON records as of 2019-09-16

Author(s): Stian Soiland-Reyes; Paul Groth
Published in: Zenodo

CWLProv – Interoperable retrospective provenance capture and its challenges

Author(s): European Commission; Farah Zaib Khan; Stian Soiland-Reyes; Michael R. Crusoe; Andrew Lonie; Richard O. Sinnott
Published in: Faculty of 1000 Research Ltd

HADDOCK screening against human Angiotensin Converting Enzyme 2 (ACE2)

Author(s): P. I. Koukos; M. Réau; A. M. J. J. Bonvin
Published in: Zenodo

HADDOCK screening against the COVID-19 RNA dependent RNA polymerase (RdRp)

Author(s): P. I. Koukos; Réau, M.; Bonvin, A. M. J. J.
Published in: Zenodo

HADDOCK pharmacophore-based screening against the COVID-19 main protease (Mpro)

Author(s): P. I. Koukos; Réau, M.; Bonvin, A. M. J. J.
Published in: Zenodo

HADDOCK shape-based screening against the COVID-19 main protease (Mpro)

Author(s): P. I. Koukos; M. Réau; A. M. J. J. Bonvin
Published in: Zenodo

Illuminating Two-Component Signaling with Model Bacteriophytochromes

Author(s): Elina Multamäki, Rahul Nanekar
Published in: Zenodo

Illuminating Two-Component Signaling with Model Bacteriophytochromes

Author(s): Elina Multamäki, Rahul Nanekar, Dmitry Morozov, Topias Lievonen, David Golonka, Weixiao Yuan Wahlgren, Brigitte Stucki-Buchli, Jari Rossi, Vesa Hytönen, Sebastian Westenhoff, Janne Ihalainen, Andreas Möglich, Heikki Takala
Published in: Zenodo

Software

BioExcel exascale co-design benchmark cases

Author(s): Berk Hess; Rodrigo Varga Honorato; Alexandre Bonvin; Arno Proeme; Mark Abraham
DOI: 10.5281/zenodo.3354706; 10.5281/zenodo.3354707
Publisher: Zenodo

Third project release of BioExcel core applications

Author(s): Berk Hess
DOI: 10.5281/zenodo.3906456; 10.5281/zenodo.3906457
Publisher: Zenodo

HADDOCK v3.0.alpha2

Author(s): Honorato, Rodrigo; Jiménez-García, Brian; Bonvin, Alexandre
DOI: 10.5281/zenodo.3883889; 10.5281/zenodo.3883888
Publisher: Zenodo

GROMACS 2021.3 Source code

Author(s): Lindahl; Abraham; Hess; van der Spoel
DOI: oai:zenodo.org:5053201; 10.5281/zenodo.5053201
Publisher: Zenodo

GROMACS 2021.2 Source code

Author(s): Lindahl; Abraham; Hess; van der Spoel
DOI: oai:zenodo.org:4723562; 10.5281/zenodo.4723562
Publisher: Zenodo

GROMACS 2019.4 Source code

Author(s): Lindahl; Abraham; Hess; van der Spoel
DOI: 10.5281/zenodo.3460414; 10.5281/zenodo.4054979; 10.5281/zenodo.4457626; 10.5281/zenodo.3562495; 10.5281/zenodo.3562494; 10.5281/zenodo.4420785; 10.5281/zenodo.3243833; 10.5281/zenodo.3685919; 10.5281/zenodo.2424362; 10.5281/zenodo.3685922; 10.5281/zenodo.3577986; 10.5281/zenodo.2424363; 10.5281/zenodo.2564764; 10.5281/zenodo.4723562; 10.5281/zenodo.3923645; 10.5281/zenodo.3773801; 10.5281/zenodo.4561626; 10.5281/zenodo.2636382; 10.5281/zenodo.4457625; 10.5281/zenodo.4576055
Publisher: Zenodo