Sequence search methods and scoring functions for the design of protein structures.
This chapter focuses on the methods developed for the automatic or semiautomatic design of protein structures. We present several algorithms for the exploration of the sequence space and scoring of the designed models. There are now several successful designs that have been achieved using these approaches such as the stabilization of a protein fold, the stabilization of a protein-protein complex interface, and the optimization of a protein function. A rapid presentation of the methodologies is followed by a detailed analysis of two test case studies. The first one deals with the redesign of a protein hydrophobic core and the second one with the stabilization of a protein structure through mutations at the surface. The different approaches are compared and the consistency of the predictions with the experimental data are discussed. All the programs tested in these protocols are freely available through the internet and may be applied to a wide range of design issues.
Madaoui
Hocine
H
Département de Biologie Joliot-Curie, CEA Saclay, Gif-sur-Yvette, France.
Becker
Emmanuelle
E
Guerois
Raphael
R
D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D008958:Models, Molecular; D009154:Mutation; D015202:Protein Engineering / Q000379:methods; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software; D013499:Surface Properties
D011506:Proteins