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This book introduces a novel framework that can be applied to study a range of molecular motions. Currently, we use it to study the protein and RNA folding process which is critical for their functions. This folding process is difficult to observe experimentally, therefore, computational methods such as simulation are very important and useful in the study of such process. The key advantage of the method introduced in this book over other computational techniques is that this approach is fast and efficient while bridging the gap between high-level folding events and low-level folding details. This advantage is validated by comparison with other computational methods and that with with experimental studies of RNA and protein. This book includes two experimental cases that clearly show how we can predict kinetics-based functional rates of ColE1 RNAII and MS2 phage RNA and their mutants using our simulation techniques. The target audience for the book is primarily researchers and students in bioinformatics, but researchers and students in other fields of computer science and molecular biology should also find this useful.
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