PROF(1) | User Commands | PROF(1) |
prof - secondary structure and solvent accessibility predictor
prof [INPUTFILE+] [OPTIONS]
Secondary structure is predicted by a system of neural networks rating at an expected average accuracy > 72% for the three states helix, strand and loop (Rost & Sander, PNAS, 1993 , 90, 7558-7562; Rost & Sander, JMB, 1993 , 232, 584-599; and Rost & Sander, Proteins, 1994 , 19, 55-72; evaluation of accuracy). Evaluated on the same data set, PROFsec is rated at ten percentage points higher three-state accuracy than methods using only single sequence information, and at more than six percentage points higher than, e.g., a method using alignment information based on statistics (Levin, Pascarella, Argos & Garnier, Prot. Engng., 6, 849-54, 1993). PHDsec predictions have three main features:
Solvent accessibility is predicted by a neural network method rating at a correlation coefficient (correlation between experimentally observed and predicted relative solvent accessibility) of 0.54 cross-validated on a set of 238 globular proteins (Rost & Sander, Proteins, 1994, 20, 216-226; evaluation of accuracy). The output of the neural network codes for 10 states of relative accessibility. Expressed in units of the difference between prediction by homology modelling (best method) and prediction at random (worst method), PROFacc is some 26 percentage points superior to a comparable neural network using three output states (buried, intermediate, exposed) and using no information from multiple alignments.
Transmembrane helices in integral membrane proteins are predicted by a system of neural networks. The shortcoming of the network system is that often too long helices are predicted. These are cut by an empirical filter. The final prediction (Rost et al., Protein Science, 1995, 4, 521-533; evaluation of accuracy) has an expected per-residue accuracy of about 95%. The number of false positives, i.e., transmembrane helices predicted in globular proteins, is about 2%. The neural network prediction of transmembrane helices (PHDhtm) is refined by a dynamic programming-like algorithm. This method resulted in correct predictions of all transmembrane helices for 89% of the 131 proteins used in a cross-validation test; more than 98% of the transmembrane helices were correctly predicted. The output of this method is used to predict topology, i.e., the orientation of the N-term with respect to the membrane. The expected accuracy of the topology prediction is > 86%. Prediction accuracy is higher than average for eukaryotic proteins and lower than average for prokaryotes. PHDtopology is more accurate than all other methods tested on identical data sets.
If no output file option (such as --fileRdb or --fileOut) is given the RDB formatted output is written into ./INPUTFILENAME.prof where 'prof' replaces the extension of the input file. In lack of extension '.prof' is appended to the input file name.
The RDB format is self-annotating, see example outputs in /share/profphd/prof/exa.
See each keyword for more help. Most of these are likely to be broken.
Known to work.
Known to work.
Broken.
Known to work.
Many other parameters change the default for this one as a side-effect, the list is not comprehensive:
phd, nophd, /^para(3|Both|Sec|Acc|Htm|CapH|CapE|CapHE)/, /^para?/, jct
B. Rost, Sander C, Fariselli P, Casadio R, Liu J, Yachdav G, Kajan L.
prof /share/profphd/prof/exa/1ppt.hssp fileRdb=/tmp/1ppt.hssp.prof
prof /share/profphd/prof/exa/1ppt.f fileRdb=/tmp/1ppt.f.rdbProf
/share/profphd/prof/embl/phd.pl /share/profphd/prof/exa/1ppt.hssp htm fileOutPhd=/tmp/query.phdPred fileOutRdb=/tmp/query.phdRdb fileNotHtm=/tmp/query.phdNotHtm
Please report bugs at <https://rostlab.org/bugzilla3/enter_bug.cgi?product=profphd>.
prof /tmp/1a3q.hssp fileRdb=/tmp/1a3q.hssp.profRdb optJury=normal both
2018-07-13 | 1.0.42 |