title: Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility.
abstract: CONCLUSIONS
  Protein secondary structure and solvent accessibility predictions are a fundamental intermediate step towards protein structure and function prediction. We present new systems for the ab initio prediction of protein secondary structure and solvent accessibility, Porter 4.0 and PaleAle 4.0. Porter 4.0 predicts secondary structure correctly for 82.2% of residues. PaleAle 4.0's accuracy is 80.0% for prediction in two classes with a 25% accessibility threshold. We show that the increasing training set sizes that come with the continuing growth of the Protein Data Bank keep yielding prediction quality improvements and examine the impact of protein resolution on prediction performances.
  
  
  BACKGROUND
  Porter 4.0 and PaleAle 4.0 are freely available for academic users at http://distillf.ucd.ie/porterpaleale/. Up to 64 kb of input in FASTA format can be processed in a single submission, with predictions now being returned to the user within a single web page and, optionally, a single email.
authors.affiliation: School of Computer Science and Informatics and Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland.
authors.forename: Claudio
authors.initials: C
authors.lastname: Mirabello
authors.forename: Gianluca
authors.initials: G
authors.lastname: Pollastri
mesh_terms: D020407:Internet; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D012984:Software; D012997:Solvents / Q000737:chemistry*
chemical_list: D011506:Proteins; D012997:Solvents