title: BOCTOPUS: improved topology prediction of transmembrane β barrel proteins.
abstract: BACKGROUND
  Transmembrane β barrel proteins (TMBs) are found in the outer membrane of Gram-negative bacteria, chloroplast and mitochondria. They play a major role in the translocation machinery, pore formation, membrane anchoring and ion exchange. TMBs are also promising targets for antimicrobial drugs and vaccines. Given the difficulty in membrane protein structure determination, computational methods to identify TMBs and predict the topology of TMBs are important.
  
  
  RESULTS
  Here, we present BOCTOPUS; an improved method for the topology prediction of TMBs by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and HMMs account for local and global residue preferences, respectively. Based on a 10-fold cross-validation test, BOCTOPUS performs better than all existing methods, reaching a Q3 accuracy of 87%. Further, BOCTOPUS predicted the correct number of strands for 83% proteins in the dataset. BOCTOPUS might also help in reliable identification of TMBs by using it as an additional filter to methods specialized in this task.
  
  
  BACKGROUND
  BOCTOPUS is freely available as a web server at: http://boctopus.cbr.su.se/. The datasets used for training and evaluations are also available from this site.
authors.affiliation: Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, SciLifeLab, Swedish E-science Research Center, Stockholm University, SE-10691 Stockholm, Sweden.
authors.forename: Sikander
authors.initials: S
authors.lastname: Hayat
authors.forename: Arne
authors.initials: A
authors.lastname: Elofsson
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D008390:Markov Chains; D008565:Membrane Proteins / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012984:Software; D060388:Support Vector Machine
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins