RaptorX-Property: a Standalone Package for Protein Structure Property Prediction
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README

===================================
RaptorX Property Standalone Package
(v1.02) 2018.05.18
===================================

Title:
RaptorX-Property: a Standalone Package for Protein Structure Property Prediction

Author:
Sheng Wang

Email:
realbigws@gmail.com


============
Publication:
============

[1]
RaptorX-Property: a Web Server for Protein Structure Property Prediction
       Sheng Wang#*, Wei Li*, Shiwang Liu, Jinbo Xu#
                                            Nucleic Acids Research, 2016

[2]
Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields
       Sheng Wang#, Jian Peng, Jianzhu Ma, Jinbo Xu#
                                            Scientific Reports, 2016

[3]
AUCpreD: Proteome-level Protein Disorder Prediction by AUC-maximized Deep Convolutional Neural Fields
       Sheng Wang#, Jianzhu Ma, Jinbo Xu#
                                            ECCB, 2016
                                            Bioinformatics, 2016

[4]
AUC-maximized Deep Convolutional Neural Fields for Protein Sequence Labeling
       Sheng Wang, Siqi Sun, Jinbo Xu#
                                            ECML/PKDD, 2016


========
Install:
========

1. download the package

git clone https://github.com/realbigws/RaptorX_Property_Fast
cd RaptorX_Property_Fast

--------------

2. compile

cd source_code/
	make
cd ../

--------------

3. setup

./setup.pl

[note]:
before you run anything, type the above command for configuration just for once.


=========
Database:
=========

1. if databases/uniprot20 not exist, create it by 

mkdir -p databases/uniprot20


2. download the UniProt20 database from the following link:

http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/uniprot20_2016_02.tgz

uncompressed it, and move all files or symbol link to databases/uniprot20_2016_02


3. if other version of UniProt20 is applied, then use '-d uniprot20_XXXX' option in ./Fast_TGT.sh


4. note that the new UniClust30 database could also be applied, such as:
http://wwwuser.gwdg.de/~compbiol/uniclust/2017_10/uniclust30_2017_10_hhsuite.tar.gz



=======
Server:
=======

1. Please try to use our RaptorX Property server at:
http://raptorx.uchicago.edu/StructurePropertyPred/predict/


2. Users may also use the 'curl' command to submit their jobs. For example,
curl --form jobname=test_job --form email=user@domain --form sequences=ENIEVHMLNKGAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVESIKDMIPEGAEKFKSKINENYVLTVTQPGAYLVKCTPHYAMGMIALIAVGDSPANLDQIVSAKKPKIVQERLEKVIASAK http://raptorx.uchicago.edu/StructurePropertyPred/curl/

[note]: 
(i) the 'email' is NOT required.
(ii) the 'job_url' and 'down_url' will be displayed after the 'curl' command is executed.




======
Usage:
======

./oneline_command.sh <input_fasta> <out_dir> [cpu_number] [PROF_or_NOT]

-------

Here the first input argument is the input sequence in FASTA format,
the second input is the CPU number,
the third input is to use profile or not.


-------


./PDBTM_Topology_Pred.sh -i example/1bhaA.tgt -l example/1bhaA.pdbtm

The module to predict transmembrane topology.



================
Running example:
================

1. use sequence profile:
        cp example/T0530.fasta .
        cp example/T0530.tgt .
        ./oneline_command.sh T0530.fasta tmp 1 1

or,
	./oneline_command.sh example/T0530.fasta tmp 1 1

-----------------------

2. not use sequence profile:
        ./oneline_command.sh example/T0530.fasta tmp 1 0

-----------------------

The output files should be found in the tmp/T0530/ folder


=============
Output files:
=============

1. overall detailed results:
	SeqID.all

e.g., file 'T0530.all' in tmp/T0530/ folder. This file contains all the detail prediction results for Secondary Structure Element (SS3 and SS8), Solvent Accessbility (ACC), and Order/Disorder prediction (DISO)

------------------

2. detailed results in separate files:
	SeqID.ss3
	SeqID.ss8
	SeqID.acc
	SeqID.diso

These files contain the detail prediction results in the form of probability.

------------------

3. simple results in separate files:
	SeqID.ss3_simp
	SeqID.ss8_simp
	SeqID.acc_simp
	SeqID.diso_simp

These files contain the simple predicion results in onee line.

------------------