High Performance Computing for Drug Discovery and Biomedicine

ISBN-13: 9781071634486 / Angielski / Twarda / 2023

Opis

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.

Spis treści

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