A Centre of Excellence in Computational Biomedicine

Risultati finali

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.

Pubblicazioni

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

Autori: Zainab Altai, Marco Viceconti, Amaka C. Offiah, Xinshan Li
Pubblicato in: Biomechanics and Modeling in Mechanobiology, Numero 17/4, 2018, Pagina/e 1001-1009, ISSN 1617-7959
Editore: Springer Verlag
DOI: 10.1007/s10237-018-1008-9

Coarse graining molecular dynamics with graph neural networks

Autori: 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
Pubblicato in: The Journal of Chemical Physics, Numero 153/19, 2020, Pagina/e 194101, ISSN 0021-9606
Editore: American Institute of Physics
DOI: 10.1063/5.0026133

HPC compact quasi-Newton algorithm for interface problems

Autori: Alfonso Santiago, Miguel Zavala-Aké, Ricard Borrell, Guillaume Houzeaux, Mariano Vázquez
Pubblicato in: Journal of Fluids and Structures, Numero 96, 2020, Pagina/e 103009, ISSN 0889-9746
Editore: Academic Press
DOI: 10.1016/j.jfluidstructs.2020.103009

Uncertainty quantification in classical molecular dynamics

Autori: Shunzhou Wan, Robert C. Sinclair, Peter V. Coveney
Pubblicato in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numero 379/2197, 2021, ISSN 1364-503X
Editore: Royal Society of London
DOI: 10.1098/rsta.2020.0082

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

Autori: P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, A. G. Hoekstra
Pubblicato in: Biomechanics and Modeling in Mechanobiology, Numero 19/2, 2020, Pagina/e 681-692, ISSN 1617-7959
Editore: 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

Autori: P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, A. G. Hoekstra
Pubblicato in: Cardiovascular Engineering and Technology, Numero 10/4, 2019, Pagina/e 568-582, ISSN 1869-408X
Editore: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00431-4

Reducing the Complexity of Musculoskeletal Models Using Gaussian Process Emulators

Autori: Ivan Benemerito, Erica Montefiori, Alberto Marzo and Claudia Mazzà
Pubblicato in: Applied Sciences, 2022, ISSN 2076-3417
Editore: MDPI
DOI: 10.3390/app122412932

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

Autori: C. Winsor, X. Li, M. Qasim, C.R. Henak, P.J. Pickhardt, H. Ploeg, M. Viceconti
Pubblicato in: Bone, Numero 143, 2021, Pagina/e 115759, ISSN 8756-3282
Editore: 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

Autori: David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Pubblicato in: Advanced Theory and Simulations, Numero 3/1, 2019, Pagina/e 1900194, ISSN 2513-0390
Editore: John Wiley & Sons
DOI: 10.1002/adts.201900194

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

Autori: Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Pubblicato in: Chemical Science, Numero 11/4, 2020, Pagina/e 1140-1152, ISSN 2041-6520
Editore: Royal Society of Chemistry
DOI: 10.1039/c9sc03754c

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

Autori: Hector Martinez-Navarro, Ana Mincholé, Alfonso Bueno-Orovio, Blanca Rodriguez
Pubblicato in: Scientific Reports, Numero 9/1, 2019, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-019-53221-2

SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Autori: Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis
Pubblicato in: Journal of Chemical Information and Modeling, Numero 60/6, 2020, Pagina/e 2673-2677, ISSN 1549-9596
Editore: 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

Autori: Christos Kotsalos, Jonas Latt, Bastien Chopard
Pubblicato in: Journal of Computational Physics, Numero 398, 2019, Pagina/e 108905, ISSN 0021-9991
Editore: Academic Press
DOI: 10.1016/j.jcp.2019.108905

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

Autori: Britt J. M. van Rooij, Gábor Závodszky, Alfons G. Hoekstra, David N. Ku
Pubblicato in: Scientific Reports, Numero 10/1, 2020, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-020-74518-7

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

Autori: Alexander Heifetz, Inaki Morao, M. Madan Babu, Tim James, Michelle W. Y. Southey, Dmitri G. Fedorov, Matteo Aldeghi, Michael J. Bodkin, Andrea Townsend-Nicholson
Pubblicato in: Journal of Chemical Theory and Computation, Numero 16/4, 2020, Pagina/e 2814-2824, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.9b01136

TorchMD: A Deep Learning Framework for Molecular Simulations

Autori: Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Pubblicato in: Journal of Chemical Theory and Computation, Numero 17/4, 2021, Pagina/e 2355-2363, ISSN 1549-9618
Editore: 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

Autori: 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
Pubblicato in: Computer Methods in Applied Mechanics and Engineering, Numero 361, 2020, Pagina/e 112762, ISSN 0045-7825
Editore: 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

Autori: 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
Pubblicato in: Royal Society Open Science, Numero 7/2, 2020, Pagina/e 191752, ISSN 2054-5703
Editore: Royal Society Publishing
DOI: 10.1098/rsos.191752

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

Autori: Sharp Chim Yui Lo, J. W. S. McCullough, P. V. Coveney
Pubblicato in: Scientific Reports, 2022, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-022-21923-9

DeltaDelta neural networks for lead optimization of small molecule potency

Autori: José Jiménez-Luna, Laura Pérez-Benito, Gerard Martínez-Rosell, Simone Sciabola, Rubben Torella, Gary Tresadern, Gianni De Fabritiis
Pubblicato in: Chemical Science, Numero 10/47, 2019, Pagina/e 10911-10918, ISSN 2041-6520
Editore: Royal Society of Chemistry
DOI: 10.1039/c9sc04606b

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

Autori: Adrià Pérez, Pablo Herrera-Nieto, Stefan Doerr, Gianni De Fabritiis
Pubblicato in: Journal of Chemical Theory and Computation, Numero 16/7, 2020, Pagina/e 4685-4693, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.0c00205#

Finite element analysis informed variable selection for femoral fracture risk prediction

Autori: Mark Taylor, Marco Viceconti, Pinaki Bhattacharya, Xinshan Li
Pubblicato in: Journal of the Mechanical Behavior of Biomedical Materials, Numero 118, 2021, Pagina/e 104434, ISSN 1751-6161
Editore: Elsevier BV
DOI: 10.1016/j.jmbbm.2021.104434

Computational prediction of GPCR oligomerization

Autori: Andrea Townsend-Nicholson, Nojood Altwaijry, Andrew Potterton, Inaki Morao, Alexander Heifetz
Pubblicato in: Current Opinion in Structural Biology, Numero 55, 2019, Pagina/e 178-184, ISSN 0959-440X
Editore: Elsevier BV
DOI: 10.1016/j.sbi.2019.04.005

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

Autori: Andrew Potterton, Fouad S. Husseini, Michelle W. Y. Southey, Mike J. Bodkin, Alexander Heifetz, Peter V. Coveney, Andrea Townsend-Nicholson
Pubblicato in: Journal of Chemical Theory and Computation, Numero 15/5, 2019, Pagina/e 3316-3330, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.8b01270

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

Autori: Mateusz K. Bieniek, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Pubblicato in: Journal of Chemical Theory and Computation, Numero 17/2, 2021, Pagina/e 1250-1265, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.0c01179

Spherization of red blood cells and platelet margination in COPD patients

Autori: 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
Pubblicato in: Annals of the New York Academy of Sciences, Numero 1485/1, 2021, Pagina/e 71-82, ISSN 0077-8923
Editore: New York Academy of Sciences
DOI: 10.1111/nyas.14489

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

Autori: Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Matteo Aldeghi, Laurie Sarrat, Dmitri G Fedorov, Mike J Bodkin, Andrea Townsend-Nicholson
Pubblicato in: Current Opinion in Structural Biology, Numero 55, 2019, Pagina/e 85-92, ISSN 0959-440X
Editore: 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

Autori: Alexander Gheorghiu, Peter V. Coveney, Alya A. Arabi
Pubblicato in: Physical Chemistry Chemical Physics, Numero 23/10, 2021, Pagina/e 6252-6265, ISSN 1463-9076
Editore: Royal Society of Chemistry
DOI: 10.1039/d0cp06218a

Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations

Autori: Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Pubblicato in: Journal of Chemical Information and Modeling, Numero 60/10, 2020, Pagina/e 5003-5010, ISSN 1549-9596
Editore: 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

Autori: Z. Altai, M. Viceconti, X. Li, A.C. Offiah
Pubblicato in: Clinical Radiology, Numero 75/1, 2020, Pagina/e 78.e9-78.e16, ISSN 0009-9260
Editore: 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

Autori: Andrea Townsend-Nicholson
Pubblicato in: Interface Focus, Numero 10/6, 2020, Pagina/e 20200003, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0003

Hierarchically Structured Bioinspired Nanocomposites

Autori: 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
Pubblicato in: Nature Materials, 2022, ISSN 1476-4660
Editore: Nature
DOI: 10.1038/s41563-022-01384-1

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

Autori: Shunzhou Wan, Gary Tresadern, Laura Pérez‐Benito, Herman Vlijmen, Peter V. Coveney
Pubblicato in: Advanced Theory and Simulations, Numero 3/1, 2019, Pagina/e 1900195, ISSN 2513-0390
Editore: John Wiley & Sons
DOI: 10.1002/adts.201900195

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

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

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

Autori: Peter V. Coveney, Roger R. Highfield
Pubblicato in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numero 379/2197, 2021, ISSN 1364-503X
Editore: Royal Society of London
DOI: 10.1098/rsta.2020.0067

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

Autori: Marco Viceconti, Muhammad Qasim, Pinaki Bhattacharya, Xinshan Li
Pubblicato in: Current Osteoporosis Reports, Numero 16/3, 2018, Pagina/e 216-223, ISSN 1544-1873
Editore: Current Science Inc.
DOI: 10.1007/s11914-018-0438-8

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

Autori: D. Groen, H. Arabnejad, D. Suleimenova, W. Edeling, E. Raffin, Y. Xue, K. Bronik, N. Monnier, P. V. Coveney
Pubblicato in: Computer Physics Communications, 2022, ISSN 0010-4655
Editore: 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

Autori: Zainab Altai, Muhammad Qasim, Xinshan Li, Marco Viceconti
Pubblicato in: Clinical Biomechanics, Numero 68, 2019, Pagina/e 137-143, ISSN 0268-0033
Editore: 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

Autori: Sha Li, Bastien Chopard, Jonas Latt
Pubblicato in: Journal of Computational Science, Numero 38, 2019, Pagina/e 101045, ISSN 1877-7503
Editore: Elsevier BV
DOI: 10.1016/j.jocs.2019.101045

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

Autori: Peter V. Coveney, Roger R. Highfield
Pubblicato in: Journal of Computational Science, Numero 46, 2020, Pagina/e 101093, ISSN 1877-7503
Editore: 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

Autori: B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, D. N. Ku
Pubblicato in: Interface Focus, Numero 11/1, 2021, Pagina/e 20190126, ISSN 2042-8898
Editore: 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

Autori: Zainab Altai, Erica Montefiori, Bart van Veen, Margaret A. Paggiosi, Eugene V. McCloskey, Marco Viceconti, Claudia Mazzà, Xinshan Li
Pubblicato in: PLOS ONE, Numero 16/2, 2021, Pagina/e e0245121, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0245121

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

Autori: Philip W. Fowler
Pubblicato in: Interface Focus, Numero 10/6, 2020, Pagina/e 20190141, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0141

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

Autori: 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
Pubblicato in: Interface Focus, Numero 11/1, 2021, Pagina/e 20190119, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0119

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

Autori: Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V. Coveney
Pubblicato in: Interface Focus, Numero 10/6, 2020, Pagina/e 20190128, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0128

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

Autori: Benjamin Csippa, Dániel Gyürki, Gábor Závodszky, István Szikora, György Paál
Pubblicato in: Cardiovascular Engineering and Technology, Numero 11/1, 2020, Pagina/e 1-13, ISSN 1869-408X
Editore: 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

Autori: Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Pubblicato in: Scientific Reports, Numero 10/1, 2020, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-020-69322-2

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

Autori: Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, Omolola Eniola-Adefeso
Pubblicato in: PLOS Computational Biology, Numero 16/3, 2020, Pagina/e e1007716, ISSN 1553-7358
Editore: PLOS
DOI: 10.1371/journal.pcbi.1007716

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

Autori: Christos Kotsalos, Jonas Latt, Joel Beny, Bastien Chopard
Pubblicato in: Interface Focus, Numero 11/1, 2021, Pagina/e 20190116, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0116

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

Autori: A. Wade, A. P. Bhati, S. Wan, P. V. Coveney
Pubblicato in: J. Chem. Theory Comput, 2022, ISSN 1549-9626
Editore: ACS
DOI: 10.1021/acs.jctc.2c00114

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

Autori: B. J. M. van Rooij, G. Závodszky, V. W. Azizi Tarksalooyeh, A. G. Hoekstra
Pubblicato in: Journal of The Royal Society Interface, Numero 16/159, 2019, Pagina/e 20190148, ISSN 1742-5689
Editore: The Royal Society
DOI: 10.1098/rsif.2019.0148

A Heterogeneous Multi-scale Model for Blood Flow

Autori: Benjamin Czaja, Gábor Závodszky, Alfons Hoekstra
Pubblicato in: Computational Science – ICCS 2020 - 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020, Proceedings, Part VI, Numero 12142, 2020, Pagina/e 403-409, ISBN 978-3-030-50432-8
Editore: Springer International Publishing
DOI: 10.1007/978-3-030-50433-5_31

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

Autori: Alexander Heifetz, Andrea Townsend-Nicholson
Pubblicato in: Quantum Mechanics in Drug Discovery, Numero 2114, 2020, Pagina/e 177-186, ISBN 978-1-0716-0281-2
Editore: Springer US
DOI: 10.1007/978-1-0716-0282-9_12

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

Autori: Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, Andrea Townsend-Nicholson
Pubblicato in: Quantum Mechanics in Drug Discovery, Numero 2114, 2020, Pagina/e 163-175, ISBN 978-1-0716-0281-2
Editore: Springer US
DOI: 10.1007/978-1-0716-0282-9_11

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Autori: Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, Dmitri G. Fedorov
Pubblicato in: Quantum Mechanics in Drug Discovery, Numero 2114, 2020, Pagina/e 187-205, ISBN 978-1-0716-0281-2
Editore: Springer US
DOI: 10.1007/978-1-0716-0282-9_13

Conformational Searching with Quantum Mechanics

Autori: Matthew Habgood, Tim James, Alexander Heifetz
Pubblicato in: Quantum Mechanics in Drug Discovery, Numero 2114, 2020, Pagina/e 207-229, ISBN 978-1-0716-0281-2
Editore: Springer US
DOI: 10.1007/978-1-0716-0282-9_14

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