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Title | Static benchmarking of membrane helix predictions. |
Publication Type | Journal Article |
Year of Publication | 2003 |
Authors | Kernytsky, A, Rost, B |
Journal | Nucleic Acids Res |
Volume | 31 |
Issue | 13 |
Pagination | 3642-4 |
Date Published | 2003 Jul 1 |
ISSN | 1362-4962 |
Keywords | Hydrophobic and Hydrophilic Interactions, Internet, Membrane Proteins, Protein Structure, Secondary, Reproducibility of Results, Sequence Analysis, Protein, Software, User-Computer Interface |
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. |
Alternate Journal | Nucleic Acids Res. |
PubMed ID | 12824384 |
PubMed Central ID | PMC168939 |
Grant List | 1-R01-LM07329-01 / LM / NLM NIH HHS / United States R01-GM63029-01 / GM / NIGMS NIH HHS / United States |