We have developed a number of tools that you might find useful:
SLEP: An automatic method for identifying surface proteins in bacteria:
PIGS: Prediction of Immunoglobulin Structures
Maistas: Prediction of structure of alternative splicing isoforms in eukaryotic genomes
http://www.bioinformatica.crs4.org/maistas/
PMDB: A database of manually built models
MOVIN: PPI interaction maps analyis tool
Meps and MapMep: Mapping epitopes on protein surfaces
Please let us know if you encounter any problem in using them...



Tools