LRFragLib: A Fragment Library Building Software for Fragment Assembly in Protein Structure Prediction
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Current Version: 1.0
By Tong Wang ----- April 2016



INSTALLATION
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LRFragLib has two precompiled released version (compiled by gcc version 4.4.7 on ubuntu): LRFragLib.linux32, which could be executed on a 32bit Linux system and LRFragLib.linux64,which could be executed on a 64bit Linux system.

Users could also compile the software:

$ g++ ./src/Parameters.h ./src/LRFragLib.cpp -fopenmp -o LRFragLib

This will generate the executable file "LRFragLib".



DEPENDENCIES
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LRFragLib does not require any other software to be executed.

However, LRFragLib requires 3 input files and another optional file:

1. PDB_ID.fasta.txt: The fasta sequence of the target protein.

2. PDB_ID.fasta.ss: The predicted secondary structure of the target protein generated by PSIPRED. Users could use PSIPRED online server at https://bioinf.cs.ucl.ac.uk/psipred/ ,and rename the output file as PDB_ID.fasta.ss. Also ,a local version of PSIPRED could be downloaded at https://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/ .

3. PDB_ID.fasta.phipsi: The predicted torsion angles of the target protein generated by SPIDER2. Users could use SPIDER2 online server at https://sparks-lab.org/yueyang/server/SPIDER2/ , and rename the output file as PDB_ID.fasta.phipsi. Also ,a local version of SPIDER2 could be downloaded at https://sparks-lab.org/yueyang/download/index.php?Download=SPIDER2_local.tgz .

4. PDB_ID.homol (optional): A file records blast result between our software database containing 4931 peptide chains and the target protein. It is essential to exclude homologous protein. To generate the file, blastpgp is used and the command is as follows:

$ blastpgp -i PDB_ID.fasta.txt -d 4931lib > PDB_ID.homol

Users should put all these files in the same directory, such as "./examples" and ensure that these files have the same formats of corresponding files in "./examples".  



EXAMPLE USAGE
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An example is in "./examples". To generate the fragment library, type the command as follows:

$ ./LRFragLib.linux64  PDB_ID

After a period of time, two result files will be generated. PDB_ID.lib records detailed information during computation. PDB_ID.frag records dihedral angles and is similar with output file by NNMake in Rosetta.



CONFIGURATION
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Users could change parameters, such as the input file directory, the output file directory or choice of exclusion of homologous proteins in "./src/Parameters.h" and compile the software.



OTHER INFORMATION
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PDB files of each fragment with 7-10 residues in FD4931 are also available for download at https://166.111.152.91/Downloads.html

Due to the limitation of file size on github, files in “Database” can be downloaded at https://166.111.152.91/Downloads/LRFragLib


TROUBLESHOOTING
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Please contact [email protected] for any problems users may encounter using LRFragLib.