ABSTRACT
Much of computational biophysics and biochemistry is aimed at making predictions of protein structure, dynamics, and function. Most prediction methods are at least in part knowledge-based rather than being derived entirely from the principles of physics. For instance, in comparative modeling of protein structure, each step in the process-from homolog identification and sequence-structure alignment to loop and side-chain modeling-is dominated by information derived from the protein sequence and structure databases (see Chapter 14). In molecular dynamics simulations, the potential energy function is based partly on conformational analysis of known peptide and protein structures and thermodynamic data (see Chapter 2).
