In order to propose a reliable model for Brucella porin topology, several 
structure prediction methods were evaluated in their ability to predict porin 
topology. Four porins of known structure were selected as test-cases and their 
secondary structure delineated. The specificity and sensitivity of 11 methods 
were separately evaluated. Our critical assessment shows that some secondary 
structure prediction methods (PHD, Dsc, Sopma) originally designed to predict 
globular protein structure are useful on porin topology prediction. The overall 
best prediction is obtained by combining these three "generalist" methods with a 
transmembrane beta strand prediction technique. This "consensus" method was 
applied to Brucella porins Omp2b and Omp2a, sharing no sequence homology with 
any other porin. The predicted topology is a 16-stranded antiparallel beta 
barrel with Omp2a showing a higher number of negatively charged residue in the 
exposed loops than Omp2b. Experiments are in progress to validate the proposed 
topology and the functional hypotheses. The ability of the proposed consensus 
method to predict topology of complex outer membrane protein is briefly 
discussed.