High Performance Computing for Drug Discovery and Biomedicine

Buch | Hardcover

429 Seiten

2023 | 2024 ed.
Springer-Verlag New York Inc.
978-1-0716-3448-6 (ISBN)

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This volume explores the application of high-performance computing (HPC) technologies to computational drug discovery (CDD) and biomedicine. The first section collects CDD approaches that, together with HPC, can revolutionize and automate drug discovery process, such as knowledge graphs, natural language processing (NLP), Bayesian optimization, automated virtual screening platforms, alchemical free energy workflows, fragment-molecular orbitals (FMO), HPC-adapted molecular dynamic simulation (MD-HPC), and the potential of cloud computing for drug discovery. The second section delves into computational algorithms and workflows for biomedicine, featuring an HPC framework to assess drug-induced arrhythmic risk, digital patient applications relevant to the clinic, virtual human simulations, cellular and whole-body blood flow modeling for stroke treatments, prediction of the femoral bone strength from CT data, and many more subjects. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary software and tools, step-by-step and readily reproducible modeling protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, High Performance Computing for Drug Discovery and Biomedicine allows a diverse audience, including computer scientists, computational and medicinal chemists, biologists, clinicians, pharmacologists and drug designers, to navigate the complex landscape of what is currently possible and to understand the challenges and future directions of HPC-based technologies.

lt;p>1. Introduction to Computational Biomedicine

Shunzhou Wan and Peter V. Coveney

2. Introduction to High Performance Computing

Marco Verdicchio and Carlos Teijeiro Barjas

3. Computational Biomedicine (CompBioMed) Centre of Excellence: Selected Key Achievements

Gavin J. Pringle

4. In Silico Clinical Trials: Is It Possible?

Simon Arsène, Yves Parès, Eliott Tixier, Solène Granjeon-Noriot, Bastien Martin, Lara Bruezière, Claire Couty, Eulalie Courcelles, Riad Kahoul, Julie Pitrat, Natacha Go, Claudio Monteiro, Julie Kleine-Schultjann, Sarah Jemai, Emmanuel Pham, Jean-Pierre Boissel, and Alexander Kulesza

5. Bayesian Optimization in Drug Discovery

Lionel Colliandre and Christophe Muller

6. Automated Virtual Screening

Vladimir Joseph Sykora

7. The Future of Drug Development with Quantum Computing

Bhushan Bonde, Pratik Patil, and Bhaskar Choubey

8. Edge, Fog, and Cloud Against Disease: The Potential of High-Performance Cloud Computing for Pharma Drug Discovery

Bhushan Bonde

9. Knowledge Graphs and Their Applications in Drug Discovery

Tim James and Holger Hennig

10. Natural Language Processing for Drug Discovery Knowledge Graphs: Promises and Pitfalls

J. Charles G. Jeynes, Tim James, and Matthew Corney

11. Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities

Anna M. Herz, Tahsin Kellici, Inaki Morao, and Julien Michel

12. Molecular Dynamics and Other HPC Simulations for Drug Discovery

Martin Kotev and Constantino Diaz Gonzalez

13. High Throughput Structure-Based Drug Design (HT-SBDD) Using Drug Docking, Fragment Molecular Orbital Calculations, and Molecular Dynamic Techniques

Reuben L. Martin, Alexander Heifetz, Mike J. Bodkin, and Andrea Townsend-Nicholson

14. HPC Framework for Performing In Silico Trials Using a 3D Virtual Human Cardiac Population as Means to Assess Drug-Induced Arrhythmic Risk

Jazmin Aguado-Sierra, Renee Brigham, Apollo K. Baron, Paula Dominguez Gomez, Guillaume Houzeaux, Jose M. Guerra, Francesc Carreras, David Filgueiras-Rama, Mariano Vazquez, Paul A. Iaizzo, Tinen L. Iles, and Constantine Butakoff

15. Effect of Muscle Forces on Femur during Level Walking Using a Virtual Population of Older Women

Zainab Altai, Erica Montefiori, and Xinshan Li

16. Cellular Blood Flow Modeling with HemoCell

Gabor Zavodszky, Christian Spieker, Benjamin Czaja, and Britt van Rooij

17. A Blood Flow Modeling Framework for Stroke Treatments

Remy Petkantchin, Franck Raynaud, Karim Zouaoui Boudjeltia, and Bastien Chopard

18. Efficient and Reliable Data Management for Biomedical Applications

Ivan Pribec, Stephan Hachinger, Mohamad Hayek, Gavin J. Pringle, Helmut

Brüchle, Ferdinand Jamitzky, and Gerald Mathias

19. Accelerating COVID-19 Drug Discovery with High-Performance Computing

Alexander Heifetz

20. Teaching Medical Students to Use Supercomputers: A Personal Reflection

Andrea Townsend-Nicholson

Erscheinungsdatum	16.09.2023
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	XIII, 429 p.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Mathematik / Informatik ► Informatik ► Theorie / Studium
	Informatik ► Weitere Themen ► Bioinformatik
	Medizin / Pharmazie ► Medizinische Fachgebiete ► Biomedizin
	Medizin / Pharmazie ► Medizinische Fachgebiete ► Pharmakologie / Pharmakotherapie
	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
Schlagworte	Artificial Intelligence and Machine Learning • Cloud Computing • Computational drug discovery (CDD) • drug design • HPC • In silico biomedicine • Personalized medicine • Precision medicine
ISBN-10	1-0716-3448-8 / 1071634488
ISBN-13	978-1-0716-3448-6 / 9781071634486
Zustand	Neuware