Protein Structure Prediction as a Systems Problem
Protein structure prediction is a complex problem, which requires various types of techniques to solve different aspects of the problem. To address this complexity, a large number of computational methods have been developed, as discussed in the previous chapters of this book. When the protein structure prediction problem was first formulated, it was envisioned that one could computationally predict any protein structure through solving a minimization problem of a unified physical energy function since protein folding is governed by laws of physics. Such an approach is referred to as “ab initio” protein structure prediction (Tanaka and Scheraga, 1977; States et al., 1980; Chapter 13 of this book). While appealing and theoretically achievable, such ab initio methods only have a limited practical value for the purpose of structure prediction as of now due to the inadequacy of current physical models and the significant gap between the required computing power and what is currently available, among other issues.
KeywordsProtein Data Bank Structure Prediction System Problem Protein Structure Prediction Query Protein
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