The FALC (Fragment Assembly and Loop Closure) program for modeling missing regions in proteins
(Written by Lim Heo, July 2013)
FALC.tar.gz (531MB, Linux 64bit only, md5sum check: 0c16fec86be651e798ad5682e2ae9e13)
- 2014. 11. 06: Update FALC source code (more optimized src).
- 2014. 04. 29: Troubles in reading BLAST checkpoint file fixed.
- 2013. 12. 05: Bugs and library dependency problem fixed.
How to use FALC
1. Untar FALC.tar.gz, and check the contents.
>tar xzf FALC.tar.gz
There should be the following directories and files in the FALC directory.
2. Execute setup.py for installation
- setup.py: script file for installation
- db: several blast and GALAXY related database files
- bin: binary files for building fragments and FALC
- lib: library files for running FALC
- templates: template files for running FALC
- defined: template input for running FALC
- example: an example for using FALC
- utils: additional binary files for FALC
This makes "$HOME/.galaxy" directory to define an environment suitable for running FALC.
This step should be taken by all FALC users.
3. Modify the configuration file
and find the line starting with "BLAST_HOME" and enter your BLAST path.
If your absolute path of "blastpgp" is "/data/blast/blast-2.2.26/bin/blastpgp",
your BLAST path is "/data/blast/blast-2.2.26".
- Model generation
1. Preparing input files
FALC requires three input files: a sequence file, a PDB file, and a file for assigning modeling
2. Running FALC
The whole protein sequence must be provided in the FASTA format.
This file must contain the loop or terminal sequences to be modelled.
One-letter alphabets for twenty standard amino acids are allowed in the file, but
no "X" or "-" are allowed. Comments starting with ">" are also allowed.
A protein structure file must be provided in the
It is recommended that the coordinates of all residues except for the loop or terminal residues to be modelled are provided.
If there are additional residues without coordinates, they are automatically filled up.
HETATM lines are ignored.
ULR (Unreliable Local Region) file (file for assigning modeling regions)
The regions for modeling must be provided in the following ULR format.
"Index ULR_type res_start-res_end 0.000"
Up to 10 ULR regions can be modeled at a time.
1 L 45-66 0.000
2 T 1-10 0.000
specifies two ULR regions to be modelled, a loop and the N-terminus.
- Index: Serial number for the ULR region
- ULR_type: 'T' for terminus and 'L' for non-terminal loop
- res_start: The residue number of the first residue of the ULR region
- res_end: The residue number of the final residue of the ULR region
- The length for each ULR region should be longer than 4 residues.
If input files are prepared, execute the script ($FALC/bin/falc.py) as follows:
>$FALC/bin/falc.py -title [TITLE] -pdb [Input PDB] -fa [Input SEQ] -ulr [Input ULR]
-n [# of output models]
This command makes a directory named [TITLE]. All FALC processes are performed in this
directory. Therefore, the [TITLE] should not be the same as any existing directory name.
The FALC builds [# of output models] models for the regions defined in [Input ULR] file
from [Input PDB] with sequence [Input SEQ].
>$FALC/bin/falc.py -title F0001 -pdb F0001.pdb -fa F0001.fa -ulr F0001.ulr -n 20
builds 20 models from "F0001.pdb" with sequence "F0001.fa" for the regions defined in
"F0001.ulr", and the predicted models are placed in the "F0001/model" directory.
The predicted models are placed in the "model" directory. The residue numbers in the files are adjusted
so that the residue number for the first residue is 1, so there may be changes if your input PDB file does not start with residue 1.
- J. Ko, D. Lee, H. Park, E. A. Coutsias, J. Lee, and C. Seok, The FALC-Loop web server for protein loop
modeling, Nucleic Acids Res. 39, W210-W214 (2011).
- J. Lee, D. Lee, H. Park, E. A. Coutsias, and C. Seok, Protein loop modeling by using fragment assembly and
analytical loop closure, Proteins: Structure, Function, and Bioinformatics, 78, 3428-3436 (2010).
- E. A. Coutsias, C. Seok, M. P. Jacobson, and K. A. Dill, A Kinematic View of Loop Closure, J. Comput. Chem.
25, 510-528 (2004).