Intro and Install | FAQ | Command Line

Tools

prospect		Primary tool for protein threading. Includes pthread support to speed up threading against a library on a multi-core system
prospect_mpi		An MPI enabled version of Prospect, threads multiple templates on different computers simlatiously
prospect_convert		Sort and convert alignments output by prospect
prospect2modeller		Convert a set of prospect files into a modeller run
prospect_psipred.pl		Perl Script to run PsiPred secondary structure prediction and convert the results to the SSP format
template_gen.pl		A Perl Script Generate your own threading template based on a PDB file
template_gen.py		A Python Script to Generate your own threading templates based on a PDB file (this one is considered to be more 'current')
get_chk_file.pl		Generate a checkpoint file with PsiBlast
read_chk		Parse the checkpoint file output by PsiBlast

Tool Examples

prospect_psipred.pl d1ash__.seq

Run BlastPGP on a FASTA file, then run PsiPred to predict the secondary structure, and then convert the data to a format usable by prospect

prospect -fssp d1ash_.ssp -o out.d1ash__.xml

Run prospect on the SSP file d1ash__.ssp, and save the results in out.d1ash_.xml

prospect_convert out.d1ash__.xml -list -raw

List contents of out.d1ash__.xml, sorted by RawScore

template_gen.py d1ash__.ent > d1ash__.xml

Generate a template file for the PDB file d1ash__.ent

prospect -fssp d1ash__.ssp -ftemplate d1ash__.xml -o out.d1ash__.xml

Run prospect on the SSP file d1ash__.ssp against the specific template d1ash__.xml and save the results in out.d1ash__.xml

prospect -fxml d1ash__.xml -ftlist test.list -o out.d1ash__.xml -ncpus 1:2 -zscore -zscore_full -zcycles 100 -zscore_energy -wname vardel -oweights

Run prospect on the xml file d1ash__.xml against the template list in file test.list and output to out.d1ash__.xml. The multiprocessing option should do one threading at a time, but use 2 processors when possible (usually when calculating the zscore). A request to calculate the lite zscore and the full zscore, and do a sampling of 100 decoys. Also include the zscore energy in the file output as well as the weight parameters that were used. Also use the weight parameter set that include the variable deletion model.

prospect2modeller -t test out.d1ash__.xml d1jboa_ my_modeller_dir

Convert the alignment to d1jboa_ in out.d1ash__.xml to the files needed to do a modeller run inside the directory my_modeller_dir. Name the modeller target 'test'.

Prospect Command Line Arguments

-fssp <file path>        : The SSP file of the target to be threaded
-ftemplate <file path>   : The xml file of the template 
                           the target is to be threaded against

-frestart <file path>    : The output xml file to resume 
                           a set of threadings from

-zscore                  : Calculate and output the Zscore
-zscore_full             : Calculate and output the Zscore Full

-ainteger                : Use the integer programming methods 
                           to solve threading problems

-fseq : Fasta formated sequence input
-fphd : PHD formated secondary structure prediction input
-ffreq : Freq (text version of a chk file) formatted input
-fssp : SSP secondary structure prediction formatted input
-frestart : XML file to resume threading list
-fdist : Distance definitions (test code)
-fconf : Configuration file (expired)
-o : Output file path
-qname : Define target name
-ftlist : File listing the templates to be threaded against
-ftemplate : Specific template file to be threaded against
-tname : Find template in path by name
-help : Print instructions
-zscore : Calculate the zscore
-zscore_full : Calculate the zscore using the 'full' calculation (rethread shuffled decoys using dynamic programming)
-zscore_energy : Calculate the zscores of the individual energies
-zcycles : Number of samples to try with zscore calculations
-filter : Attempt to shrink the alignment problem by filtering out bad places to put cores (TEST CODE)
-noloop : Don't include loop regions in calculating the energy against the template (TEST CODE)
-adynamic : Use the dynamic programming algorithm to calculate the alignment (DEFAULT)
-ainteger : Use the integer programming algorithm to calculate the alignment
-ainteger_div : (TEST CODE)
-ainteger_gtmip : (TEST CODE)
-ainteger_sift : (TEST CODE)
-ainteger_coredel : Use the integer programming algorithm to calculate the alignment, with an expanded model that allows for core deletions
-atreedecomp : (TEST CODE)
-fork : Fork before doing the threading, thus if there is a crash, the main app won't die
-ncpus : Expand out to multiple CPUs, using pThreads
-max_mem : (TEST CODE)
-wmutation : Adjust the weight parameter of the Mutation energy
-wmutationlog : Adjust the weight parameter of the Mutation Log energy
-wsingleton : Adjust the weight parameter of the Singleton energy
-wsec_struct : Adjust the weight parameter of the Secondary Structure energy
-wgap : Adjust the weight parameter of the Gap energy
-wcoredel : Adjust the weight parameter of the Core Deletion energy
-wtwobody : Adjust the weight parameter of the Twobody cuttoff energy
-wthreebody : Adjust the weight parameter of the threebody energy (TEST CODE)
-wfourbody : Adjust the weight parameter of the fourbody energy (TEST CODE)
-wgonnet : Adjust the weight parameter of the Gonnet energy
-wtwobody_frozen : Adjust the weight parameter of the Frozen twobody energy
-wdfire : Adjust the weight parameter of the Dfire distance dependent twobody energy
-wdistconst : Adjust the weight parameter of the Distance constraint energy (TEST CODE)
-simple_twobody : Use a simple assignment comparison, rather then the matrix mulitple for calculating twobody score (TEST CODE)
-oweights : Include the Energy Weight parameters used to produce the alignment in the output file
-otimeinfo : (BROKEN)
-otemplate_loc : (EXPIRED)
-ochk :
-opdb : (EXPIRED)
-obackbone : (TEST CODE)
-v : Verbosity level 1
-vv : Verbosity level 2
-vvv : Verbosity level 3

Prospect Convert

Prospect Convert has the ability to parse equations based on values of the different features for protein alignments. This feature is primarily for integrating with machine learning based fold recognition techniques.

prospect_convert out.d1ash__.xml -lformat "%sn %sr %sz"

List all of the templates with name raw score and zscore.

List of Feature names

sa    -    score average

sr    -    score raw

srz   -    score raw zscore

sz    -    score z

sf    -    score zfull

sn    -    score neural network

sel   -    score z mutation log

se1   -    score z singleton

ses   -    score z secondary structure

se2   -    score z twobody

sed   -    score z dfire


su0    -    score user defined

su1    -    score user defined

su2    -    score user defined

su3    -    score user defined

szm    -    score z mean

szs    -    score z sd

sfm    -    score zfull mean

sfs    -    score zfull sd

selm   -    score z mutation log mean

sels   -    score z mutation log sd

se1m   -    score z singleton mean

se1s   -    score z singleton sd

sesm   -    score z secondary structure mean

sess   -    score z secondary structure sd

se2m   -    score z twobody mean

se2s   -    score z twobody sd

sedm   -    score z dfire mean

seds   -    score z dfire sd

    //features

ft    -    template length

fq    -    target length

fc    -    core count

fm    -    core residue count

fr    -    length ratio (fq/ft)

fR    -    length ratio (ft/fq)

    //alignment info

an    -    num align res

aN    -    % align res

ac    -    num align core

aC    -    % align core

ai    -    num align ident res

aI    -    % align ident res

am    -    num align core res

aM    -    % align core res

a2c   -    num contact pairs

a2d   -    num half contact pairs

af    -    num target alignment fragments

    //weights

wm    -    mutation weight

wl    -    mutation log weight

w1    -    singleton weight

ws    -    secondary struct weight

w2    -    twobody weight

wd    -    dfire weight

wo    -    gap open weight

we    -    gap const weight

wt    -    coredel weight

wa    -    template singledel weight

wi    -    template singleins weight

wqa   -    target singledel weight

wqi   -    target singleins weight

wc    -    contactdel weight

    //energy

em    -    mutation energy

el    -    mutation log energy

e1    -    singleton energy

es    -    secondary struct energy

e2    -    twobody energy

ed    -    dfire energy

et    -    coredel energy

eo    -    gap open energy

ee    -    gap const energy

ea    -    template singledel energy

ei    -    template singleins energy

eqa   -    target singledel energy

eqi   -    target singleins energy

ec    -    contactdel energy

emw   -    mutation energy * weight

elw   -    mutation log energy * weight

e1w   -    singleton energy * weight

esw   -    secondary struct energy * weight

e2w   -    twobody energy * weight

edw   -    dfire energy * weight

etw   -    coredel energy * weight

eow   -    gap open energy * weight

ecw   -    gap const energy * weight

eaw   -    template singledel energy * weight

eiw   -    template singleins energy * weight

eqaw  -    query singledel energy * weight

eqiw  -    query singleins energy * weight