SUMMARY: 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.
AVAILABILITY: 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.