Protein Structure Prediction

Protein structure prediction has matured over the past few years to the point that even fully automated methods can provide reasonably accurate three-dimensional models of protein structures. However, until now it has not been possible to develop programs able to perform as well as human experts, who are still capable of systematically producing better models than automated servers. Although the precise details of protein structure prediction procedures are different for virtually every protein, this chapter describes a generic procedure to obtain a three-dimensional protein model starting from the amino acid sequence. This procedure takes advantage both of programs and servers that have been shown to perform best in blind tests and of the current knowledge about evolutionary relationships between proteins, gained from detailed analyses of protein sequence, structure, and functional data.