PROFphd
========

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:

   1. improved accuracy through evolutionary information from multiple sequence alignments
   2. improved beta-strand prediction through a balanced training procedure
   3. more accurate prediction of secondary structure segments by using a multi-level system

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. 


To run PROFphd with example input, type:

prof  <PROF_ROOT>/exa/1ppt.f

where <PROF_ROOT> will be the location of your PRFOphd installation
[ default: /usr/share/profphd/prof ]

COMMAND LINE OPTIONS

	3               
	       predict sec + acc + htm          (see each keyword for more help)

	acc
	       predict solvent accessibility, only

	ali             
	       add alignment to 'human-readable' PROF output file(s)

	arch   
	       system architecture (e.g.: SGI64|SGI5|SGI32|SUNMP|ALPHA)

	ascii          
	       write 'human-readable' PROF output file(s)

	best   
	       PROF with best accuracy and longest run-time

	both
               predict secondary structure and solvent accessibility

	data           
	       data=<all|brief|normal|detail>  for HTML out: only those parts of predictions written

	debug          
	       keep most intermediate files

	doEval
	       DO evaluation for list (only for known structures and lists)

	doFilterHssp    
	       filter the input HSSP file       (excluding some pairs)

	doHtmfil        	
	       DO filter the membrane prediction                  (default)

	doHtmisit
	      DO check strength of predicted membrane helix      (default)

	doHtmref
	      DO refine the membrane prediction                  (default)

	doHtmtop
	     DO membrane helix topology                         (default)

	dssp
             convert PROF into DSSP format

	expand
	     expand insertions when converting output to MSF format

	fast 
             PROF with lowest accuracy and highest speed

	fileCasp
	       name of PROF output in CASP format              (file.caspProf)

	fileDssp
	       name of PROF output in DSSP format              (file.dsspProf)

	fileHtml
	       name of PROF output in HTML format              (file.htmlProf)

	fileMsf
	       name of PROF output in MSF format               (file.msfProf)

	fileNotHtm
	       name of file flagging that no membrane helix was found

	fileProf
	       name of PROF output in human readable format    (file.prof)

	fileRdb
	       name of PROF output in RDB format               (file.rdbProf)

	fileSaf         
	       name of PROF output in SAF format               (file.safProf)

	filter
	       filter the input HSSP file       (excluding some pairs)

	good
               PROF with good accuracy and moderate speed

	graph
               add ASCII graph to 'human-readable' PROF output file(s)

	htm
               use: 'htm=<N|0.N>' gives minimal transmembrane helix detected default is 'htm=8' (resp. htm=0.8)  smaller numbers more false positives and fewer false negatives!

	html   argument         
	       'hmtl' or 'html=<all|body|head>' write HTML format of prediction 'html' will result in that the PROF output is converted to HTML 'html=body' restricts HTML file to the HTML_BODY tag part 'html=head' restricts HTML file to the HTML_HEADER tag part 'html=all'  gives both HEADER and BODY

	keepConv
	       keep the conversion of the input file to HSSP format
	       
	keepFilter argument
	     <*|doKeepFilter=1>     keep the filtered HSSP file
	
	keepHssp  argument
	       <*|doKeepHssp=1>         keep the intermediate HSSP file
	
	keepNetDb argument
	     <*|doKeepNetDb=1>       keep the intermediate DbNet file(s)
	
	list argument
	           <*|isList=1>      input file is list of files

	msf   
	         convert PROF into MSF format

	nice            
	       give 'nice-D' to set the nice value (priority) of the job
	
	noProfHead
	      do NOT copy file with tables into local directory
	
	noSearch
	     short for doSearchFile=0, i.e. no searching of DB files
	
	noascii
	     surpress writing ASCII (i.e. human readable) result files
	
	nohtml
	         surpress writing HTML result files
	
	nonice
	         job will not be niced, i.e. not run with lower priority
	
	notEval
	        DO NOT check accuracy even when known structures
	
	notHtmfil
	        do NOT filter the membrane prediction
	
	notHtmisit      
	       do NOT check whether or not membrane helix strong enough

	notHtmref
	      do NOT refine the membrane prediction
	
	notHtmtop
	      do NOT membrane helix topology
	
	s_k_i_p
	        problems,manual,hints,notation,txt,known,DONE,Date,date,aa,Lhssp,numaa,code
	
	saf
               convert PROF into SAF format

	scrAddHelp      
	
	scrGoal
	        neural network switching
	
	scrHelpTxt
	     Input file formats accepted:       hssp,dssp,msf,saf,fastamul,pirmul,fasta,pir,gcg,swiss

	scrIn
          list_of_files (or single file) parameter_file

	scrName
	        prof
	
	scrNarg
	        2
	
	sec
            predict secondary structure,   only

	silent
         	no information written to screen
	
	skipMissing	
	       do not abort if input file missing!

	sourceFile
	     prof

	test
           is just a test (faster)

	tst
            quick run through program, low accuracy

	user
            user name



PARAMETERS

  abbrProf3          abbrProfAcc        abbrProfBoth       abbrProfHtm        
  abbrProfRdb        abbrProfSec        acc2Symbol         acc2Thresh         
  acc3Symbol         acc3Thresh         accBuriedSat       aliMinLen          
  bitacc             blastConvTemperature confProf           convOtherDistance  
  convPfar           debug              debugali           debugfor           
  dirBin             dirBlastMat        dirData            dirDataBlastbin    
  dirDssp            dirEMBL            dirFssp            dirHome            
  dirHssp            dirMat             dirNet             dirOut             
  dirPar             dirProf            dirScr             dirScrLib          
  dirSwiss           dirWork            doCorSparse        doEval             
  doFilter           doFilterAcc        doKeepFilter       doKeepHssp         
  doKeepNetDb        doRetAliExpand     doRetAscii         doRetCasp          
  doRetDssp          doRetHeader        doRetHtml          doRetMsf           
  doRetPhd1994       doRetRdb           doRetSaf           doSkipExisting     
  doSkipMissing      errPrd_docorr      errPrd_dodetail    errPrd_doinfo      
  errPrd_domatrix    errPrd_domatthews  errPrd_doq10       errPrd_doq2        
  errPrd_doq3        errPrd_dori        errPrd_dosov       errPrd_title       
  exeConvHssp2saf    exeConvertSeqFor   exeCopf            exeCopfPack        
  exeFilterHssp      exeFilterHsspFor   exeFilterHsspPack  exeHtmfil          
  exeHtmref          exeHtmtop          exeLibProfCol      exeLibProfErr      
  exeLibProfHtml     exeLibProfMain     exeLibProfWrt      exePhd1994         
  exePhd1994For      exeProfFor         exePvmgetarch      exeSysNice         
  exeSysNiceMAC     extBlastMat        extChain           extDssp            
  extFasta           extFastamul        extGcg             extHssp            
  extHssp4acc        extHssp4htm        extHsspFil         extMsf             
  extNetIn           extNetOut          extNotHtm          extOutEval         
  extOutTmp          extPir             extPirmul          extProfDssp        
  extProfHtml        extProfJct         extProfMsf         extProfOut         
  extProfPar         extProfRdb         extProfSaf         extSaf             
  extSwiss           fileHelpHints      fileHelpMan        fileHelp        
  fileHelpProblems   fileMatBlosum62    fileMatBlosum62psi fileMatGcg         
  fileMatHsspFilter  fileMatMcLachlan   fileOutError       fileOutErrorBlast  
  fileOutErrorChain  fileOutErrorConv   fileOutScreen      fileOutSeqTmp      
  fileOutTmp         fileOutTrace       fileOutWarn        formRepeat         
  formatRetAli       headProf3          headProfAcc        headProfBoth       
  headProfConcise    headProfHtm        headProfSec        isList             
  jobid              mapHELBGT         mapHELBGT1       mapHELBGT2       
  mapHELBGT3       mapHELBGT4       mapHELBGT5       mapHELBGT6       
  maptransHELBGT    modeAli            modeFileIn         modeObs            
  modeRunNet         modeSec            modeSec6           netlevelMax        
  nresPerLineAli     nresPerRow         nresPerRowAli      nresPerRowHtml     
  Acc10Filter     Acc10Filter2    DoHtmfil        DoHtmisit       
  DoHtmref        DoHtmtop        Filter          FilterAcc       
  Hssp2msf        HtmisitMin      Jury            ModeRetHtml     
  ModeRetHtmlDef  Nice            NiceDef         OutAli          
  OutAverages     OutBrief        OutDetail       OutGraph        
  OutHeader       OutHeaderInfo   OutHeaderSum    OutNormal       
  OutNotation     OutSubset       OutTxtPreRow    Prof            
  Prof2msf        ProfQuality     SecFilterE      SecFilterH      
  para3              para3Tst           para3runbest       para3runfast       
  para3rungood       paraAcc            paraAccTst         paraAccrunbest     
  paraAccrunfast     paraAccrungood     paraBoth           paraBothTst        
  paraBothrunbest    paraBothrunfast    paraBothrungood    paraHtm            
  paraSec            paraSecTst         paraSecrunbest     paraSecrunfast     
  paraSecrungood     preOut             rdbHdrSimple       rdbHyphen          
  rdbSep             rdbWhite           riAddNophd         riCapFlip          
  riSubAcc           riSubHtm           riSubSec           riSubSym           
  secCapNon1         secCapSeg1         secCapSeg2         secCapSym          
  secCapSymEcap      secCapSymHEcap     secCapSymHcap      secCapSymNon       
  srsPath            symbolChainAny     symbolPrdShort     symbolResidueUnk   
  thresh2acc         title              titleIni           titleNetIn         
  titleNetOut        titleTmp           urlpp             verb2              
  verb3              verbAli            verbForErr         verbForProt        
  verbForSam         verbForVec         verbose            windowUsed     



AUTHOR
       Burkahrd Rost, Christ Sander, P Fariselli & R Casadio, Jinfeng Liu, Guy Yachdav, Laszlo Kajan

INTERNET RESOURCES
       Main website:  http://www.predictprotein.org/
       Documentation:  http://www.predictprotein.org/docs.php
       Community website:  http://groups.google.com/group/PredictProtein
       FTP:  ftp://rostlab.org/pub/cubic/downloads/prof
       Module repository:  
       Newsgroups: http://groups.google.com/group/PredictProtein

Copyright (C) 1992,1993,1994,1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004
2005, 2006, 2007, 2008,2009 ROSTLAB

BIG
===
'exe normal' is the normal compilation node comment line
'exe big' is the comment that designates the '*_big' compliation option section

