ABSTRACT
Computational methods play a range of roles in protein engineering from the simple use of visualization to guide rational design to fully automated de novo design algorithms. In the next chapters, many of these approaches will be discussed. Here we will focus on the former, that is, computational methods that complement human insight in rational protein engineering. The approaches can loosely be grouped into three classes: (1) methods based on analysis of primary sequence; (2) the visual analysis of protein structure; and (3) fast estimation of mutational effects. The mechanistic details of performing sequence and structural analysis have been extensively discussed in other texts, and thus the focus here is on the application of these approaches. The approaches discussed here all involve use of software that is either available as a Web service or as a freely available, downloadable program. The Web locations of key tools are summarized in the tables.
