A Centre of Excellence in Computational Biomedicine

Livrables

Definition of the incubation plan, description of its components and implementation strategy. Software documentation and usage summary. Best practice for documentation, regression tests, benchmarking, etc.

Second Report on Fast Track Applications

Second report on research outcomes from fast track applications including a first best practices section to help external users of the underlying codes to quickly set up their own applications eg in the context of task 24

Dissemination Action Plan

A detailed and comprehensive report on the dissemination actions that will be carried out by the project.

Intermediate Report on VVUQ, Exemplar Research Integration and Community Applications

This report will describe the results of VVUQ technique application in Task 25 and the exemplar integration research as well as review achievements with community application codes

CompBioMed2 Compute and Data Services Strategic Plan

This deliverable will define of the strategies for the design of services portfolio and the operational service processes needed for the maintenance and delivery of CompBioMed compute and data services.

First Report on VVUQ Strategies and Community Application Codes

This report will describe the VVUQ strategies and techniques developed in Task 25 and review the community application codes with best prospects for parallelisation and deployment by Task 24

Project Handbook

WP1 will produce a project handbook outlining the project’s procedures, legal obligations and reporting processes, to assist each partner.

First Report on Fast Track Application Readiness

Report on the applications and research being undertaken within the CompBioMed2 environment based on the initial, Fast Track deployment.

Report on Dissemination and Innovation

A report on dissemination and innovation activities produced by the project at the midterm point

Quality Assurance Plan

To manage the project’s quality control process, a Quality Assurance Plan will be created to assist internal reviewers in monitoring all deliverables before they are finalised and submitted to the Commission. The deliverable will also contain a detailed risk analysis and contingency planning.

Report on Establishment of the Community Engagement

A report on the report on the establishment of the users’ engagement portal and of the HPC-M community of practice.

Ethics Report

This report will be initiated in M6 and maintained as a running log of the types of data used in CompBioMed2. The report will keep detailed information on the procedures for data collection, storage, protection, retention, and destruction, and confirmation that they comply with national and EU legislation.

Advanced Report on Biomedical Applications

Technical report on results of code improvement focussing on robustness efficiency usability etc Report on software incubation

Report on Maintenance and Development of CompBioMed Computational Services

This report will describe the status of the CompBioMed service portfolio at the halfway point of the project lifetime For each of the identified services we will provide a technical description of its components access mechanism used and einfrastructure usage

Analytics Requirements Analysis

This report will assess the potential for applying analytics techniques to CompBioMed2 project data

Innovation Plan

A detailed innovation plan, to be adhered to by all members of the consortium, to promote the innovation and commercialisation aspects of this project.

Data Management Plan

Task 3.1 will produce an initial Data Management Plan for the project. This will be updated over the course of the project as its needs evolve.

Publications

Investigating the mechanical response of paediatric bone under bending and torsion using finite element analysis

Auteurs: Zainab Altai, Marco Viceconti, Amaka C. Offiah, Xinshan Li
Publié dans: Biomechanics and Modeling in Mechanobiology, Numéro 17/4, 2018, Page(s) 1001-1009, ISSN 1617-7959
Éditeur: Springer Verlag
DOI: 10.1007/s10237-018-1008-9

Coarse graining molecular dynamics with graph neural networks

Auteurs: Brooke E. Husic, Nicholas E. Charron, Dominik Lemm, Jiang Wang, Adrià Pérez, Maciej Majewski, Andreas Krämer, Yaoyi Chen, Simon Olsson, Gianni de Fabritiis, Frank Noé, Cecilia Clementi
Publié dans: The Journal of Chemical Physics, Numéro 153/19, 2020, Page(s) 194101, ISSN 0021-9606
Éditeur: American Institute of Physics
DOI: 10.1063/5.0026133

HPC compact quasi-Newton algorithm for interface problems

Auteurs: Alfonso Santiago, Miguel Zavala-Aké, Ricard Borrell, Guillaume Houzeaux, Mariano Vázquez
Publié dans: Journal of Fluids and Structures, Numéro 96, 2020, Page(s) 103009, ISSN 0889-9746
Éditeur: Academic Press
DOI: 10.1016/j.jfluidstructs.2020.103009

Uncertainty quantification in classical molecular dynamics

Auteurs: Shunzhou Wan, Robert C. Sinclair, Peter V. Coveney
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 379/2197, 2021, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0082

A particle-based model for endothelial cell migration under flow conditions

Auteurs: P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, A. G. Hoekstra
Publié dans: Biomechanics and Modeling in Mechanobiology, Numéro 19/2, 2020, Page(s) 681-692, ISSN 1617-7959
Éditeur: Springer Verlag
DOI: 10.1007/s10237-019-01239-w

Location-Specific Comparison Between a 3D In-Stent Restenosis Model and Micro-CT and Histology Data from Porcine In Vivo Experiments

Auteurs: P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, A. G. Hoekstra
Publié dans: Cardiovascular Engineering and Technology, Numéro 10/4, 2019, Page(s) 568-582, ISSN 1869-408X
Éditeur: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00431-4

Reducing the Complexity of Musculoskeletal Models Using Gaussian Process Emulators

Auteurs: Ivan Benemerito, Erica Montefiori, Alberto Marzo and Claudia Mazzà
Publié dans: Applied Sciences, 2022, ISSN 2076-3417
Éditeur: MDPI
DOI: 10.3390/app122412932

Evaluation of patient tissue selection methods for deriving equivalent density calibration for femoral bone quantitative CT analyses

Auteurs: C. Winsor, X. Li, M. Qasim, C.R. Henak, P.J. Pickhardt, H. Ploeg, M. Viceconti
Publié dans: Bone, Numéro 143, 2021, Page(s) 115759, ISSN 8756-3282
Éditeur: Elsevier BV
DOI: 10.1016/j.bone.2020.115759

Application of the ESMACS Binding Free Energy Protocol to a Multi‐Binding Site Lactate Dehydogenase A Ligand Dataset

Auteurs: David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Publié dans: Advanced Theory and Simulations, Numéro 3/1, 2019, Page(s) 1900194, ISSN 2513-0390
Éditeur: John Wiley & Sons
DOI: 10.1002/adts.201900194

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

High arrhythmic risk in antero-septal acute myocardial ischemia is explained by increased transmural reentry occurrence

Auteurs: Hector Martinez-Navarro, Ana Mincholé, Alfonso Bueno-Orovio, Blanca Rodriguez
Publié dans: Scientific Reports, Numéro 9/1, 2019, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-019-53221-2

SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Auteurs: Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis
Publié dans: Journal of Chemical Information and Modeling, Numéro 60/6, 2020, Page(s) 2673-2677, ISSN 1549-9596
Éditeur: American Chemical Society
DOI: 10.1021/acs.jcim.0c00143

Bridging the computational gap between mesoscopic and continuum modeling of red blood cells for fully resolved blood flow

Auteurs: Christos Kotsalos, Jonas Latt, Bastien Chopard
Publié dans: Journal of Computational Physics, Numéro 398, 2019, Page(s) 108905, ISSN 0021-9991
Éditeur: Academic Press
DOI: 10.1016/j.jcp.2019.108905

Biorheology of occlusive thrombi formation under high shear: in vitro growth and shrinkage

Auteurs: Britt J. M. van Rooij, Gábor Závodszky, Alfons G. Hoekstra, David N. Ku
Publié dans: Scientific Reports, Numéro 10/1, 2020, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-74518-7

Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method

Auteurs: Alexander Heifetz, Inaki Morao, M. Madan Babu, Tim James, Michelle W. Y. Southey, Dmitri G. Fedorov, Matteo Aldeghi, Michael J. Bodkin, Andrea Townsend-Nicholson
Publié dans: Journal of Chemical Theory and Computation, Numéro 16/4, 2020, Page(s) 2814-2824, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.9b01136

TorchMD: A Deep Learning Framework for Molecular Simulations

Auteurs: Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Publié dans: Journal of Chemical Theory and Computation, Numéro 17/4, 2021, Page(s) 2355-2363, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.0c01343

Sensitivity analysis of a strongly-coupled human-based electromechanical cardiac model: Effect of mechanical parameters on physiologically relevant biomarkers

Auteurs: F. Levrero-Florencio, F. Margara, E. Zacur, A. Bueno-Orovio, Z.J. Wang, A. Santiago, J. Aguado-Sierra, G. Houzeaux, V. Grau, D. Kay, M. Vázquez, R. Ruiz-Baier, B. Rodriguez
Publié dans: Computer Methods in Applied Mechanics and Engineering, Numéro 361, 2020, Page(s) 112762, ISSN 0045-7825
Éditeur: Elsevier BV
DOI: 10.1016/j.cma.2019.112762

Fluid–structure interaction simulations outperform computational fluid dynamics in the description of thoracic aorta haemodynamics and in the differentiation of progressive dilation in Marfan syndrome patients

Auteurs: R. Pons, A. Guala, J. F. Rodríguez-Palomares, J. C. Cajas, L. Dux-Santoy, G. Teixidó-Tura, J. J. Molins, M. Vázquez, A. Evangelista, J. Martorell
Publié dans: Royal Society Open Science, Numéro 7/2, 2020, Page(s) 191752, ISSN 2054-5703
Éditeur: Royal Society Publishing
DOI: 10.1098/rsos.191752

Parametric Analysis of an Efficient Boundary Condition to Control Outlet Flow Rates in Large Arterial Networks

Auteurs: Sharp Chim Yui Lo, J. W. S. McCullough, P. V. Coveney
Publié dans: Scientific Reports, 2022, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-022-21923-9

DeltaDelta neural networks for lead optimization of small molecule potency

Auteurs: José Jiménez-Luna, Laura Pérez-Benito, Gerard Martínez-Rosell, Simone Sciabola, Rubben Torella, Gary Tresadern, Gianni De Fabritiis
Publié dans: Chemical Science, Numéro 10/47, 2019, Page(s) 10911-10918, ISSN 2041-6520
Éditeur: Royal Society of Chemistry
DOI: 10.1039/c9sc04606b

AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations

Auteurs: Adrià Pérez, Pablo Herrera-Nieto, Stefan Doerr, Gianni De Fabritiis
Publié dans: Journal of Chemical Theory and Computation, Numéro 16/7, 2020, Page(s) 4685-4693, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.0c00205#

Finite element analysis informed variable selection for femoral fracture risk prediction

Auteurs: Mark Taylor, Marco Viceconti, Pinaki Bhattacharya, Xinshan Li
Publié dans: Journal of the Mechanical Behavior of Biomedical Materials, Numéro 118, 2021, Page(s) 104434, ISSN 1751-6161
Éditeur: Elsevier BV
DOI: 10.1016/j.jmbbm.2021.104434

Computational prediction of GPCR oligomerization

Auteurs: Andrea Townsend-Nicholson, Nojood Altwaijry, Andrew Potterton, Inaki Morao, Alexander Heifetz
Publié dans: Current Opinion in Structural Biology, Numéro 55, 2019, Page(s) 178-184, ISSN 0959-440X
Éditeur: Elsevier BV
DOI: 10.1016/j.sbi.2019.04.005

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A 2A Receptor Binders

Auteurs: Andrew Potterton, Fouad S. Husseini, Michelle W. Y. Southey, Mike J. Bodkin, Alexander Heifetz, Peter V. Coveney, Andrea Townsend-Nicholson
Publié dans: Journal of Chemical Theory and Computation, Numéro 15/5, 2019, Page(s) 3316-3330, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.8b01270

TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing

Auteurs: Mateusz K. Bieniek, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Publié dans: Journal of Chemical Theory and Computation, Numéro 17/2, 2021, Page(s) 1250-1265, ISSN 1549-9618
Éditeur: American Chemical Society
DOI: 10.1021/acs.jctc.0c01179

Spherization of red blood cells and platelet margination in COPD patients

Auteurs: Karim Zouaoui Boudjeltia, Christos Kotsalos, Daniel Ribeiro Sousa, Alexandre Rousseau, Christophe Lelubre, Olivier Sartenaer, Michael Piagnerelli, Jérôme Dohet‐Eraly, Frank Dubois, Nicole Tasiaux, Bastien Chopard, Alain Van Meerhaeghe
Publié dans: Annals of the New York Academy of Sciences, Numéro 1485/1, 2021, Page(s) 71-82, ISSN 0077-8923
Éditeur: New York Academy of Sciences
DOI: 10.1111/nyas.14489

Characterising GPCR–ligand interactions using a fragment molecular orbital-based approach

Auteurs: Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Matteo Aldeghi, Laurie Sarrat, Dmitri G Fedorov, Mike J Bodkin, Andrea Townsend-Nicholson
Publié dans: Current Opinion in Structural Biology, Numéro 55, 2019, Page(s) 85-92, ISSN 0959-440X
Éditeur: Elsevier BV
DOI: 10.1016/j.sbi.2019.03.021

The influence of external electric fields on proton transfer tautomerism in the guanine–cytosine base pair

Auteurs: Alexander Gheorghiu, Peter V. Coveney, Alya A. Arabi
Publié dans: Physical Chemistry Chemical Physics, Numéro 23/10, 2021, Page(s) 6252-6265, ISSN 1463-9076
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d0cp06218a

Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations

Auteurs: Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Publié dans: Journal of Chemical Information and Modeling, Numéro 60/10, 2020, Page(s) 5003-5010, ISSN 1549-9596
Éditeur: American Chemical Society
DOI: 10.1021/acs.jcim.0c00381

Investigating rolling as mechanism for humeral fractures in non-ambulant infants: a preliminary finite element study

Auteurs: Z. Altai, M. Viceconti, X. Li, A.C. Offiah
Publié dans: Clinical Radiology, Numéro 75/1, 2020, Page(s) 78.e9-78.e16, ISSN 0009-9260
Éditeur: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.crad.2019.08.026

Educating and engaging new communities of practice with high performance computing through the integration of teaching and research

Auteurs: Andrea Townsend-Nicholson
Publié dans: Interface Focus, Numéro 10/6, 2020, Page(s) 20200003, ISSN 2042-8898
Éditeur: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0003

Hierarchically Structured Bioinspired Nanocomposites

Auteurs: D. Nepal, S Kang, K. M. Adstedt, K. Kanhaiya, M. R. Bockstaller, L. C. Brinson, M. J. Buehler, P. V. Coveney, K. Dayal, J. A. El-Awady, L. C. Henderson, D. L. Kaplan, S. Keten, N. A. Kotov, G. C. Schatz, S. Vignolini, F. Vollrath, Y. Wang, B. I. Yakobson, V. V. Tsukruk, H. Heinz
Publié dans: Nature Materials, 2022, ISSN 1476-4660
Éditeur: Nature
DOI: 10.1038/s41563-022-01384-1

Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica‐Exchange

Auteurs: Shunzhou Wan, Gary Tresadern, Laura Pérez‐Benito, Herman Vlijmen, Peter V. Coveney
Publié dans: Advanced Theory and Simulations, Numéro 3/1, 2019, Page(s) 1900195, ISSN 2513-0390
Éditeur: John Wiley & Sons
DOI: 10.1002/adts.201900195

Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors

Auteurs: S. Wan, A. Bhati, D. Wright, I. Wall, A. Graves, D. Green, P. V. Coveney
Publié dans: J. Chem. Inf. Model., 2022, ISSN 1549-960X
Éditeur: ACS
DOI: 10.1021/acs.jcim.2c00255

When we can trust computers (and when we can't)

Auteurs: Peter V. Coveney, Roger R. Highfield
Publié dans: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numéro 379/2197, 2021, ISSN 1364-503X
Éditeur: Royal Society of London
DOI: 10.1098/rsta.2020.0067

Are CT-Based Finite Element Model Predictions of Femoral Bone Strengthening Clinically Useful?

Auteurs: Marco Viceconti, Muhammad Qasim, Pinaki Bhattacharya, Xinshan Li
Publié dans: Current Osteoporosis Reports, Numéro 16/3, 2018, Page(s) 216-223, ISSN 1544-1873
Éditeur: Current Science Inc.
DOI: 10.1007/s11914-018-0438-8

FabSim3: An automation toolkit for verified simulations using high performance computing

Auteurs: D. Groen, H. Arabnejad, D. Suleimenova, W. Edeling, E. Raffin, Y. Xue, K. Bronik, N. Monnier, P. V. Coveney
Publié dans: Computer Physics Communications, 2022, ISSN 0010-4655
Éditeur: Elsevier BV
DOI: 10.1016/j.cpc.2022.108596

The effect of boundary and loading conditions on patient classification using finite element predicted risk of fracture

Auteurs: Zainab Altai, Muhammad Qasim, Xinshan Li, Marco Viceconti
Publié dans: Clinical Biomechanics, Numéro 68, 2019, Page(s) 137-143, ISSN 0268-0033
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.clinbiomech.2019.06.004

Continuum model for flow diverting stents in 3D patient-specific simulation of intracranial aneurysms

Auteurs: Sha Li, Bastien Chopard, Jonas Latt
Publié dans: Journal of Computational Science, Numéro 38, 2019, Page(s) 101045, ISSN 1877-7503
Éditeur: Elsevier BV
DOI: 10.1016/j.jocs.2019.101045

From digital hype to analogue reality: Universal simulation beyond the quantum and exascale eras

Auteurs: Peter V. Coveney, Roger R. Highfield
Publié dans: Journal of Computational Science, Numéro 46, 2020, Page(s) 101093, ISSN 1877-7503
Éditeur: Elsevier BV
DOI: 10.1016/j.jocs.2020.101093

Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study

Auteurs: B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, D. N. Ku
Publié dans: Interface Focus, Numéro 11/1, 2021, Page(s) 20190126, ISSN 2042-8898
Éditeur: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0126

Femoral neck strain prediction during level walking using a combined musculoskeletal and finite element model approach

Auteurs: Zainab Altai, Erica Montefiori, Bart van Veen, Margaret A. Paggiosi, Eugene V. McCloskey, Marco Viceconti, Claudia Mazzà, Xinshan Li
Publié dans: PLOS ONE, Numéro 16/2, 2021, Page(s) e0245121, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0245121

How quickly can we predict trimethoprim resistance using alchemical free energy methods?

Auteurs: Philip W. Fowler
Publié dans: Interface Focus, Numéro 10/6, 2020, Page(s) 20190141, ISSN 2042-8898
Éditeur: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0141

Towards blood flow in the virtual human: efficient self-coupling of HemeLB

Auteurs: J. W. S. McCullough, R. A. Richardson, A. Patronis, R. Halver, R. Marshall, M. Ruefenacht, B. J. N. Wylie, T. Odaker, M. Wiedemann, B. Lloyd, E. Neufeld, G. Sutmann, A. Skjellum, D. Kranzlmüller, P. V. Coveney
Publié dans: Interface Focus, Numéro 11/1, 2021, Page(s) 20190119, ISSN 2042-8898
Éditeur: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0119

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

Auteurs: Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V. Coveney
Publié dans: Interface Focus, Numéro 10/6, 2020, Page(s) 20190128, ISSN 2042-8898
Éditeur: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0128

Hydrodynamic Resistance of Intracranial Flow-Diverter Stents: Measurement Description and Data Evaluation

Auteurs: Benjamin Csippa, Dániel Gyürki, Gábor Závodszky, István Szikora, György Paál
Publié dans: Cardiovascular Engineering and Technology, Numéro 11/1, 2020, Page(s) 1-13, ISSN 1869-408X
Éditeur: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00445-y

Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

Auteurs: Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Publié dans: Scientific Reports, Numéro 10/1, 2020, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-69322-2

The influence of red blood cell deformability on hematocrit profiles and platelet margination

Auteurs: Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, Omolola Eniola-Adefeso
Publié dans: PLOS Computational Biology, Numéro 16/3, 2020, Page(s) e1007716, ISSN 1553-7358
Éditeur: PLOS
DOI: 10.1371/journal.pcbi.1007716

Digital blood in massively parallel CPU/GPU systems for the study of platelet transport

Auteurs: Christos Kotsalos, Jonas Latt, Joel Beny, Bastien Chopard
Publié dans: Interface Focus, Numéro 11/1, 2021, Page(s) 20190116, ISSN 2042-8898
Éditeur: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0116

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility

Auteurs: A. Wade, A. P. Bhati, S. Wan, P. V. Coveney
Publié dans: J. Chem. Theory Comput, 2022, ISSN 1549-9626
Éditeur: ACS
DOI: 10.1021/acs.jctc.2c00114

Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer

Auteurs: B. J. M. van Rooij, G. Závodszky, V. W. Azizi Tarksalooyeh, A. G. Hoekstra
Publié dans: Journal of The Royal Society Interface, Numéro 16/159, 2019, Page(s) 20190148, ISSN 1742-5689
Éditeur: The Royal Society
DOI: 10.1098/rsif.2019.0148

A Heterogeneous Multi-scale Model for Blood Flow

Auteurs: Benjamin Czaja, Gábor Závodszky, Alfons Hoekstra
Publié dans: Computational Science – ICCS 2020 - 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020, Proceedings, Part VI, Numéro 12142, 2020, Page(s) 403-409, ISBN 978-3-030-50432-8
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-030-50433-5_31

Characterizing Rhodopsin-Arrestin Interactions with the Fragment Molecular Orbital (FMO) Method

Auteurs: Alexander Heifetz, Andrea Townsend-Nicholson
Publié dans: Quantum Mechanics in Drug Discovery, Numéro 2114, 2020, Page(s) 177-186, ISBN 978-1-0716-0281-2
Éditeur: Springer US
DOI: 10.1007/978-1-0716-0282-9_12

Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method

Auteurs: Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, Andrea Townsend-Nicholson
Publié dans: Quantum Mechanics in Drug Discovery, Numéro 2114, 2020, Page(s) 163-175, ISBN 978-1-0716-0281-2
Éditeur: Springer US
DOI: 10.1007/978-1-0716-0282-9_11

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Auteurs: Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, Dmitri G. Fedorov
Publié dans: Quantum Mechanics in Drug Discovery, Numéro 2114, 2020, Page(s) 187-205, ISBN 978-1-0716-0281-2
Éditeur: Springer US
DOI: 10.1007/978-1-0716-0282-9_13

Conformational Searching with Quantum Mechanics

Auteurs: Matthew Habgood, Tim James, Alexander Heifetz
Publié dans: Quantum Mechanics in Drug Discovery, Numéro 2114, 2020, Page(s) 207-229, ISBN 978-1-0716-0281-2
Éditeur: Springer US
DOI: 10.1007/978-1-0716-0282-9_14

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