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Methods in Biomolecular Modelling

Buch | Softcover

352 Seiten

2027
Elsevier - Health Sciences Division (Verlag)
978-0-443-22041-8 (ISBN)

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Methods in Biomolecular Modelling considers modeling methods with relevance to the study of biomolecular systems, including the workhorse of classical molecular dynamics and related techniques, areas where electronic structure methods find use, the higher length scales achievable through coarse grained and mesoscale methods, and combinations of scales. Applicability of methods is then illustrated with a wide range of biomolecular modeling research topics drawn from current research. Throughout the text, practical considerations of research are emphasized, including sourcing of structural data, scalability of methods on HPC systems, and linking of computation to experiment.

Part I introduces a range of modeling techniques used for biomolecular simulation, explaining the fundamental principles of each and the research areas to which they are applicable. The strengths and weaknesses of each method are outlined, along with their real-world performance on current computing resources and future trends. Part II looks at a range of application areas, with case studies illustrating the methods that can be used to investigate biomolecular systems in these areas.

Thomas Keal is a Principal Scientist in the Computational Chemistry Group at STFC Daresbury Laboratory and Honorary Professor at the UCL Department of Chemistry, UK. His research interests are in multiscale QM/MM methods and their application to problems in biomolecular and materials modelling. He completed his PhD in 2005 in the group of David Tozer at Durham University, focussing on the development of new exchange-correlation functionals for density functional theory. He then moved to a postdoctoral position in the group of Walter Thiel in Mülheim an der Ruhr, Germany, working on methods for excited state optimisation and dynamics of biomolecules. He joined Paul Sherwood’s group at Daresbury in 2008 to continue work on methods development in the ChemShell QM/MM software package, and now leads the team developing ChemShell, which is widely used in the investigation of biomolecular reaction mechanisms.

Part 1: Introduction to Biomolecular Simulation Methods
1. Molecular Dynamics with Biomolecular Force Fields
2. Free Energy Calculations
3. Enhanced Sampling Methods
4. Density Functional Theory and Ab Initio Molecular Dynamics
5. QM/MM Methods
6. Coarse Graining methods
7. Machine learning methods for biomolecules
8. The use of experimental data in biomolecular simulations

Part 2: Applications of Biomolecular Modelling
9. Protein-Ligand Interactions
10. Membrane proteins
11. Glycans and Glycoproteins
12. Intrinsically disordered proteins
13. Enzymatic reactivity
14. Nucleic acids
15. Macromolecular complexes
16. Photochemistry of biomolecules
17. Biological membranes
18. Biomaterials
19. Drug Design and Development
20. Computational Virology

Erscheint lt. Verlag	1.3.2027
Reihe/Serie	Methods in Molecular and Materials Modelling
Verlagsort	Philadelphia
Sprache	englisch
Maße	152 x 229 mm
Themenwelt	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
ISBN-10	0-443-22041-7 / 0443220417
ISBN-13	978-0-443-22041-8 / 9780443220418
Zustand	Neuware