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RaptorX-Property: a Standalone Package for Protein Structure Property Prediction
This project forked from realbigws/raptorx_property_fast
RaptorX-Property: a Standalone Package for Protein Structure Property Prediction
=================================== RaptorX Property Standalone Package (v1.02) 2018.05.18 =================================== Title: RaptorX-Property: a Standalone Package for Protein Structure Property Prediction Author: Sheng Wang Email: [email protected] ============ 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. ------------------
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