Methods in Biomolecular Modelling

This second volume in the series considers the modelling methods with greatest relevance to the study of biomolecular systems: the workhorse of classical molecular dynamics and related techniques; the areas where electronic structure methods find use; the higher length scales achievable through coarse grained and mesoscale methods; and combinations of scales. The applicability of the methods is then illustrated with a wide range of biomolecular modelling research topics drawn from the current research of leading practitioners in the field. Part I introduces a range of modelling 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 will be outlined, along with their real-world performance on current computing resources, and a pointer to future trends. The intention is to provide answers to the question: “What is method X and when should I use it?” Part II then looks at a range of application areas in more detail, with case studies illustrating the methods that can be used to investigate biomolecular systems in these areas. The intention is to provide answers to the question: “How can I use modelling to investigate problem Y?” Throughout the text practical considerations of research in these areas will be emphasised, including sourcing of structural data, scalability of methods on HPC systems, and linking of computation to experiment. Methods in Biomolecular Modelling will be invaluable for undergraduates and postgraduates who would like to understand how different biomolecular simulation techniques may be applied to a range of research topics in biochemistry and biophysics.

• Introduces a range of modelling techniques used for biomolecular simulation, explaining the fundamental principles of each and the research areas to which they are applicable
• Applications chapters in Part II provide an overview of what can be done using current methods on current computer architectures
• Practical considerations of research in these areas are emphasized, including sourcing of structural data, scalability of methods on HPC systems, and linking of computation to experiment
• Balanced explanations of the limitations of certain approaches will help beginners become confident in deciding what method to use to investigate a certain problem