A Centre of Excellence in Computational Biomedicine

Rezultaty

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.

Publikacje

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

Autorzy: Zainab Altai, Marco Viceconti, Amaka C. Offiah, Xinshan Li
Opublikowane w: Biomechanics and Modeling in Mechanobiology, Numer 17/4, 2018, Strona(/y) 1001-1009, ISSN 1617-7959
Wydawca: Springer Verlag
DOI: 10.1007/s10237-018-1008-9

Coarse graining molecular dynamics with graph neural networks

Autorzy: 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
Opublikowane w: The Journal of Chemical Physics, Numer 153/19, 2020, Strona(/y) 194101, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/5.0026133

HPC compact quasi-Newton algorithm for interface problems

Autorzy: Alfonso Santiago, Miguel Zavala-Aké, Ricard Borrell, Guillaume Houzeaux, Mariano Vázquez
Opublikowane w: Journal of Fluids and Structures, Numer 96, 2020, Strona(/y) 103009, ISSN 0889-9746
Wydawca: Academic Press
DOI: 10.1016/j.jfluidstructs.2020.103009

Uncertainty quantification in classical molecular dynamics

Autorzy: Shunzhou Wan, Robert C. Sinclair, Peter V. Coveney
Opublikowane w: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numer 379/2197, 2021, ISSN 1364-503X
Wydawca: Royal Society of London
DOI: 10.1098/rsta.2020.0082

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

Autorzy: P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, A. G. Hoekstra
Opublikowane w: Biomechanics and Modeling in Mechanobiology, Numer 19/2, 2020, Strona(/y) 681-692, ISSN 1617-7959
Wydawca: 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

Autorzy: P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, A. G. Hoekstra
Opublikowane w: Cardiovascular Engineering and Technology, Numer 10/4, 2019, Strona(/y) 568-582, ISSN 1869-408X
Wydawca: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00431-4

Reducing the Complexity of Musculoskeletal Models Using Gaussian Process Emulators

Autorzy: Ivan Benemerito, Erica Montefiori, Alberto Marzo and Claudia Mazzà
Opublikowane w: Applied Sciences, 2022, ISSN 2076-3417
Wydawca: MDPI
DOI: 10.3390/app122412932

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

Autorzy: C. Winsor, X. Li, M. Qasim, C.R. Henak, P.J. Pickhardt, H. Ploeg, M. Viceconti
Opublikowane w: Bone, Numer 143, 2021, Strona(/y) 115759, ISSN 8756-3282
Wydawca: 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

Autorzy: David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Opublikowane w: Advanced Theory and Simulations, Numer 3/1, 2019, Strona(/y) 1900194, ISSN 2513-0390
Wydawca: John Wiley & Sons
DOI: 10.1002/adts.201900194

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

Autorzy: Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Opublikowane w: Chemical Science, Numer 11/4, 2020, Strona(/y) 1140-1152, ISSN 2041-6520
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c9sc03754c

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

Autorzy: Hector Martinez-Navarro, Ana Mincholé, Alfonso Bueno-Orovio, Blanca Rodriguez
Opublikowane w: Scientific Reports, Numer 9/1, 2019, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-019-53221-2

SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Autorzy: Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis
Opublikowane w: Journal of Chemical Information and Modeling, Numer 60/6, 2020, Strona(/y) 2673-2677, ISSN 1549-9596
Wydawca: 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

Autorzy: Christos Kotsalos, Jonas Latt, Bastien Chopard
Opublikowane w: Journal of Computational Physics, Numer 398, 2019, Strona(/y) 108905, ISSN 0021-9991
Wydawca: Academic Press
DOI: 10.1016/j.jcp.2019.108905

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

Autorzy: Britt J. M. van Rooij, Gábor Závodszky, Alfons G. Hoekstra, David N. Ku
Opublikowane w: Scientific Reports, Numer 10/1, 2020, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-020-74518-7

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

Autorzy: Alexander Heifetz, Inaki Morao, M. Madan Babu, Tim James, Michelle W. Y. Southey, Dmitri G. Fedorov, Matteo Aldeghi, Michael J. Bodkin, Andrea Townsend-Nicholson
Opublikowane w: Journal of Chemical Theory and Computation, Numer 16/4, 2020, Strona(/y) 2814-2824, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.9b01136

TorchMD: A Deep Learning Framework for Molecular Simulations

Autorzy: Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Opublikowane w: Journal of Chemical Theory and Computation, Numer 17/4, 2021, Strona(/y) 2355-2363, ISSN 1549-9618
Wydawca: 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

Autorzy: 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
Opublikowane w: Computer Methods in Applied Mechanics and Engineering, Numer 361, 2020, Strona(/y) 112762, ISSN 0045-7825
Wydawca: 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

Autorzy: 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
Opublikowane w: Royal Society Open Science, Numer 7/2, 2020, Strona(/y) 191752, ISSN 2054-5703
Wydawca: Royal Society Publishing
DOI: 10.1098/rsos.191752

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

Autorzy: Sharp Chim Yui Lo, J. W. S. McCullough, P. V. Coveney
Opublikowane w: Scientific Reports, 2022, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-022-21923-9

DeltaDelta neural networks for lead optimization of small molecule potency

Autorzy: José Jiménez-Luna, Laura Pérez-Benito, Gerard Martínez-Rosell, Simone Sciabola, Rubben Torella, Gary Tresadern, Gianni De Fabritiis
Opublikowane w: Chemical Science, Numer 10/47, 2019, Strona(/y) 10911-10918, ISSN 2041-6520
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c9sc04606b

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

Autorzy: Adrià Pérez, Pablo Herrera-Nieto, Stefan Doerr, Gianni De Fabritiis
Opublikowane w: Journal of Chemical Theory and Computation, Numer 16/7, 2020, Strona(/y) 4685-4693, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.0c00205#

Finite element analysis informed variable selection for femoral fracture risk prediction

Autorzy: Mark Taylor, Marco Viceconti, Pinaki Bhattacharya, Xinshan Li
Opublikowane w: Journal of the Mechanical Behavior of Biomedical Materials, Numer 118, 2021, Strona(/y) 104434, ISSN 1751-6161
Wydawca: Elsevier BV
DOI: 10.1016/j.jmbbm.2021.104434

Computational prediction of GPCR oligomerization

Autorzy: Andrea Townsend-Nicholson, Nojood Altwaijry, Andrew Potterton, Inaki Morao, Alexander Heifetz
Opublikowane w: Current Opinion in Structural Biology, Numer 55, 2019, Strona(/y) 178-184, ISSN 0959-440X
Wydawca: Elsevier BV
DOI: 10.1016/j.sbi.2019.04.005

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

Autorzy: Andrew Potterton, Fouad S. Husseini, Michelle W. Y. Southey, Mike J. Bodkin, Alexander Heifetz, Peter V. Coveney, Andrea Townsend-Nicholson
Opublikowane w: Journal of Chemical Theory and Computation, Numer 15/5, 2019, Strona(/y) 3316-3330, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.8b01270

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

Autorzy: Mateusz K. Bieniek, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Opublikowane w: Journal of Chemical Theory and Computation, Numer 17/2, 2021, Strona(/y) 1250-1265, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.0c01179

Spherization of red blood cells and platelet margination in COPD patients

Autorzy: 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
Opublikowane w: Annals of the New York Academy of Sciences, Numer 1485/1, 2021, Strona(/y) 71-82, ISSN 0077-8923
Wydawca: New York Academy of Sciences
DOI: 10.1111/nyas.14489

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

Autorzy: Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Matteo Aldeghi, Laurie Sarrat, Dmitri G Fedorov, Mike J Bodkin, Andrea Townsend-Nicholson
Opublikowane w: Current Opinion in Structural Biology, Numer 55, 2019, Strona(/y) 85-92, ISSN 0959-440X
Wydawca: 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

Autorzy: Alexander Gheorghiu, Peter V. Coveney, Alya A. Arabi
Opublikowane w: Physical Chemistry Chemical Physics, Numer 23/10, 2021, Strona(/y) 6252-6265, ISSN 1463-9076
Wydawca: Royal Society of Chemistry
DOI: 10.1039/d0cp06218a

Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations

Autorzy: Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Opublikowane w: Journal of Chemical Information and Modeling, Numer 60/10, 2020, Strona(/y) 5003-5010, ISSN 1549-9596
Wydawca: 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

Autorzy: Z. Altai, M. Viceconti, X. Li, A.C. Offiah
Opublikowane w: Clinical Radiology, Numer 75/1, 2020, Strona(/y) 78.e9-78.e16, ISSN 0009-9260
Wydawca: 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

Autorzy: Andrea Townsend-Nicholson
Opublikowane w: Interface Focus, Numer 10/6, 2020, Strona(/y) 20200003, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0003

Hierarchically Structured Bioinspired Nanocomposites

Autorzy: 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
Opublikowane w: Nature Materials, 2022, ISSN 1476-4660
Wydawca: Nature
DOI: 10.1038/s41563-022-01384-1

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

Autorzy: Shunzhou Wan, Gary Tresadern, Laura Pérez‐Benito, Herman Vlijmen, Peter V. Coveney
Opublikowane w: Advanced Theory and Simulations, Numer 3/1, 2019, Strona(/y) 1900195, ISSN 2513-0390
Wydawca: John Wiley & Sons
DOI: 10.1002/adts.201900195

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

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

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

Autorzy: Peter V. Coveney, Roger R. Highfield
Opublikowane w: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numer 379/2197, 2021, ISSN 1364-503X
Wydawca: Royal Society of London
DOI: 10.1098/rsta.2020.0067

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

Autorzy: Marco Viceconti, Muhammad Qasim, Pinaki Bhattacharya, Xinshan Li
Opublikowane w: Current Osteoporosis Reports, Numer 16/3, 2018, Strona(/y) 216-223, ISSN 1544-1873
Wydawca: Current Science Inc.
DOI: 10.1007/s11914-018-0438-8

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

Autorzy: D. Groen, H. Arabnejad, D. Suleimenova, W. Edeling, E. Raffin, Y. Xue, K. Bronik, N. Monnier, P. V. Coveney
Opublikowane w: Computer Physics Communications, 2022, ISSN 0010-4655
Wydawca: 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

Autorzy: Zainab Altai, Muhammad Qasim, Xinshan Li, Marco Viceconti
Opublikowane w: Clinical Biomechanics, Numer 68, 2019, Strona(/y) 137-143, ISSN 0268-0033
Wydawca: 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

Autorzy: Sha Li, Bastien Chopard, Jonas Latt
Opublikowane w: Journal of Computational Science, Numer 38, 2019, Strona(/y) 101045, ISSN 1877-7503
Wydawca: Elsevier BV
DOI: 10.1016/j.jocs.2019.101045

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

Autorzy: Peter V. Coveney, Roger R. Highfield
Opublikowane w: Journal of Computational Science, Numer 46, 2020, Strona(/y) 101093, ISSN 1877-7503
Wydawca: 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

Autorzy: B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, D. N. Ku
Opublikowane w: Interface Focus, Numer 11/1, 2021, Strona(/y) 20190126, ISSN 2042-8898
Wydawca: 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

Autorzy: Zainab Altai, Erica Montefiori, Bart van Veen, Margaret A. Paggiosi, Eugene V. McCloskey, Marco Viceconti, Claudia Mazzà, Xinshan Li
Opublikowane w: PLOS ONE, Numer 16/2, 2021, Strona(/y) e0245121, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0245121

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

Autorzy: Philip W. Fowler
Opublikowane w: Interface Focus, Numer 10/6, 2020, Strona(/y) 20190141, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0141

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

Autorzy: 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
Opublikowane w: Interface Focus, Numer 11/1, 2021, Strona(/y) 20190119, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0119

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

Autorzy: Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V. Coveney
Opublikowane w: Interface Focus, Numer 10/6, 2020, Strona(/y) 20190128, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0128

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

Autorzy: Benjamin Csippa, Dániel Gyürki, Gábor Závodszky, István Szikora, György Paál
Opublikowane w: Cardiovascular Engineering and Technology, Numer 11/1, 2020, Strona(/y) 1-13, ISSN 1869-408X
Wydawca: 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

Autorzy: Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Opublikowane w: Scientific Reports, Numer 10/1, 2020, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-020-69322-2

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

Autorzy: Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, Omolola Eniola-Adefeso
Opublikowane w: PLOS Computational Biology, Numer 16/3, 2020, Strona(/y) e1007716, ISSN 1553-7358
Wydawca: PLOS
DOI: 10.1371/journal.pcbi.1007716

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

Autorzy: Christos Kotsalos, Jonas Latt, Joel Beny, Bastien Chopard
Opublikowane w: Interface Focus, Numer 11/1, 2021, Strona(/y) 20190116, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0116

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

Autorzy: A. Wade, A. P. Bhati, S. Wan, P. V. Coveney
Opublikowane w: J. Chem. Theory Comput, 2022, ISSN 1549-9626
Wydawca: ACS
DOI: 10.1021/acs.jctc.2c00114

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

Autorzy: B. J. M. van Rooij, G. Závodszky, V. W. Azizi Tarksalooyeh, A. G. Hoekstra
Opublikowane w: Journal of The Royal Society Interface, Numer 16/159, 2019, Strona(/y) 20190148, ISSN 1742-5689
Wydawca: The Royal Society
DOI: 10.1098/rsif.2019.0148

A Heterogeneous Multi-scale Model for Blood Flow

Autorzy: Benjamin Czaja, Gábor Závodszky, Alfons Hoekstra
Opublikowane w: Computational Science – ICCS 2020 - 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020, Proceedings, Part VI, Numer 12142, 2020, Strona(/y) 403-409, ISBN 978-3-030-50432-8
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-50433-5_31

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

Autorzy: Alexander Heifetz, Andrea Townsend-Nicholson
Opublikowane w: Quantum Mechanics in Drug Discovery, Numer 2114, 2020, Strona(/y) 177-186, ISBN 978-1-0716-0281-2
Wydawca: Springer US
DOI: 10.1007/978-1-0716-0282-9_12

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

Autorzy: Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, Andrea Townsend-Nicholson
Opublikowane w: Quantum Mechanics in Drug Discovery, Numer 2114, 2020, Strona(/y) 163-175, ISBN 978-1-0716-0281-2
Wydawca: Springer US
DOI: 10.1007/978-1-0716-0282-9_11

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Autorzy: Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, Dmitri G. Fedorov
Opublikowane w: Quantum Mechanics in Drug Discovery, Numer 2114, 2020, Strona(/y) 187-205, ISBN 978-1-0716-0281-2
Wydawca: Springer US
DOI: 10.1007/978-1-0716-0282-9_13

Conformational Searching with Quantum Mechanics

Autorzy: Matthew Habgood, Tim James, Alexander Heifetz
Opublikowane w: Quantum Mechanics in Drug Discovery, Numer 2114, 2020, Strona(/y) 207-229, ISBN 978-1-0716-0281-2
Wydawca: Springer US
DOI: 10.1007/978-1-0716-0282-9_14

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