Knowledge-based prediction protein modeling

This review will present an overview of current molecular mechanics techniques and discuss some of their limitations. We will then look at knowledge-based protein prediction strategies and examine the incorporation of such empirical rules into refinement methodologies for model protein systems. More comprehensive reviews of molecular dynamics simulations, knowledge-based protein modeling, and protein folding simulations are available. - " ... 

The computational approaches to predict protein structures from their amino acid sequences can be either empirical or knowledge-based. The former involves calculations of the energetically favorable structures by the use of the parameterized force fields (section 9.2) and the latter performs statistical analysis with references to the existing structures employing ranges of bioinformatic techniques (section 16.5). The comparative structural analysis leads to homologous models, which are then refined by energy minimization. 

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