title: FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.
abstract: BACKGROUND
  A number of statistical phylogenetic methods have been developed to infer conserved functional sites or regions in proteins. Many methods, e.g. Rate4Site, apply the standard phylogenetic models to infer site-specific substitution rates and totally ignore the spatial correlation of substitution rates in protein tertiary structures, which may reduce their power to identify conserved functional patches in protein tertiary structures when the sequences used in the analysis are highly similar. The 3D sliding window method has been proposed to infer conserved functional patches in protein tertiary structures, but the window size, which reflects the strength of the spatial correlation, must be predefined and is not inferred from data. We recently developed GP4Rate to solve these problems under the Bayesian framework. Unfortunately, GP4Rate is computationally slow. Here, we present an intuitive web server, FuncPatch, to perform a fast approximate Bayesian inference of conserved functional patches in protein tertiary structures.
  
  
  RESULTS
  Both simulations and four case studies based on empirical data suggest that FuncPatch is a good approximation to GP4Rate. However, FuncPatch is orders of magnitudes faster than GP4Rate. In addition, simulations suggest that FuncPatch is potentially a useful tool complementary to Rate4Site, but the 3D sliding window method is less powerful than FuncPatch and Rate4Site. The functional patches predicted by FuncPatch in the four case studies are supported by experimental evidence, which corroborates the usefulness of FuncPatch.
  
  
  METHODS
  The software FuncPatch is freely available at the web site, http://info.mcmaster.ca/yifei/FuncPatch
  
  
  BACKGROUND
  golding@mcmaster.ca
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada.
authors.forename: Yi-Fei
authors.initials: YF
authors.lastname: Huang
authors.affiliation: Department of Biology, McMaster University, Hamilton, ON L8S4K1, Canada.
authors.forename: G Brian
authors.initials: GB
authors.lastname: Golding
mesh_terms: D000595:Amino Acid Sequence; D001499:Bayes Theorem; D017124:Conserved Sequence; D006801:Humans; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins