title: Static benchmarking of membrane helix predictions.
abstract: Prediction of trans-membrane helices continues to be a difficult task with a few prediction methods clearly taking the lead; none of these is clearly best on all accounts. Recently, we have carefully set up protocols for benchmarking the most relevant aspects of prediction accuracy and have applied it to >30 prediction methods. Here, we present the extension of that analysis to the level of an automatic web server evaluating new methods (http://cubic.bioc.columbia.edu/services/tmh_benchmark/). The most important achievements of the tool are: (i) any new method is compared to the battery of well-established tools; (ii) the battery of measures explored allows spotting strengths in methods that may not be 'best' overall. In particular, we report per-residue and per-segment scores for accuracy and the error-rates for confusing membrane helices with globular proteins or signal peptides. An additional feature is that developers can directly investigate any hydrophobicity scale for its potential in predicting membrane helices.
authors.affiliation: CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. kernytsky@cubic.bioc.columbia.edu
authors.forename: Andrew
authors.initials: A
authors.lastname: Kernytsky
authors.forename: Burkhard
authors.initials: B
authors.lastname: Rost
mesh_terms: D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D008565:Membrane Proteins