title: In silico protein motif discovery and structural analysis.
abstract: A wealth of in silico tools is available for protein motif discovery and structural analysis. The aim of this chapter is to collect some of the most common and useful tools and to guide the biologist in their use. A detailed explanation is provided for the use of Distill, a suite of web servers for the prediction of protein structural features and the prediction of full-atom 3D models from a protein sequence. Besides this, we also provide pointers to many other tools available for motif discovery and secondary and tertiary structure prediction from a primary amino acid sequence. The prediction of protein intrinsic disorder and the prediction of functional sites and SLiMs are also briefly discussed. Given that user queries vary greatly in size, scope and character, the trade-offs in speed, accuracy and scale need to be considered when choosing which methods to adopt.
authors.affiliation: Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland. catherine.mooney@ucd.ie
authors.forename: Catherine
authors.initials: C
authors.lastname: Mooney
authors.forename: Norman
authors.initials: N
authors.lastname: Davey
authors.forename: Alberto J M
authors.initials: AJ
authors.lastname: Martin
authors.forename: Ian
authors.initials: I
authors.lastname: Walsh
authors.forename: Denis C
authors.initials: DC
authors.lastname: Shields
authors.forename: Gianluca
authors.initials: G
authors.lastname: Pollastri
mesh_terms: D020816:Amino Acid Motifs; D020134:Catalytic Domain; D003198:Computer Simulation; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D017510:Protein Folding; D012984:Software