From protein structure to biochemical function?
Here we describe various methods currently under development aimed at identifying a protein's function from its three-dimensional structure. We are combining a number of these methods to create a pipeline of applications, called ProFunc, which will take a given 3D structure, run all the applications on it and compile and summarise the results obtained. The aim is to provide a best guess as to the protein's function from the evidence provided by the different methods. Here we present three examples, using structures solved by the Midwest Center for Structural Genomics consortium, illustrating the strengths and weaknesses of current approaches.
Laskowski
Roman A
RA
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Watson
James D
JD
Thornton
Janet M
JM
D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D017124:Conserved Sequence; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry; D008024:Ligands; D017014:Methanobacterium / Q000737:chemistry; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D012984:Software; D013329:Structure-Activity Relationship; D020124:Thermotoga maritima / Q000737:chemistry
D001426:Bacterial Proteins; C094846:CutA protein, E coli; D004798:Enzymes; D029968:Escherichia coli Proteins; D008024:Ligands