Methods in Biomolecular Modelling, Volume Two in the series, 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.
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.
Table of Contents
PrefacePart 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
