Steps in Model Production
The homology modeling procedure can be broken down into four sequential steps: template selection, target-template alignment, model construction, and model assessment. The first two steps are often essentially performed together, as the most common methods of identifying templates rely on the production of sequence alignments; however, these alignments may not be of sufficient quality because database search techniques prioritize speed over alignment quality. These processes can be performed iteratively to improve the quality of the final model, although quality assessments that are not dependent on the true target structure are still under development.
Optimizing the speed and accuracy of these steps for use in large-scale automated structure prediction is a key component of structural genomics initiatives, partly because the resulting volume of data will be too large to process manually and partly because the goal of structural genomics requires providing models of reasonable quality to researchers who are not themselves structure prediction experts.
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