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Also see [[AdvancedOptions]]
<<importTiddlers>>
FREAD is a database search loop structure prediction protocol.

Loops are generally located in the protein’s surface and they are known to be notoriously difficult to predict.

The basic assumption of FREAD is that local sequence similarity may determine the backbone structure of a local protein structure if it is constrained within anchor structures.

FREAD predicts loops according to the following criteria:
*Cα separation of anchor structures
*~Samudrala-Moult statistical potential energy
*Local sequence similarity measured by environment specific substitution tables (specified by dihedral angles)
*Anchor structure match
FREAD gives extremely accurate results regardless of loop length if the query is identifiable in the database.

The manuscript for FREAD is found [[here|http://www3.interscience.wiley.com/journal/122688727/abstract]].
The supplementary material can be seen [[here|http://www3.interscience.wiley.com/journal/122688727/suppinfo]]

!!News

A loop test set (from soluble proteins), CASP 7 and 8 model structures and loop definitions are downloadable ([[Download|Loop Test Set]]).
Yoonjoo Choi

Oxford Protein Informatics Group (OPIG)
Department of Statistics
1 South Parks Road
Oxford ~OX1 3TG
United Kingdom

http://www.stats.ox.ac.uk/research/bioinfo
Office: +44) 1865 281247
Mobile: +44) 7912 676475
Email
##choi [at] stats [dot] ox [dot] ac [dot] uk
##yoonjoo.choi [at] stx [dot] ox [dot] ac [dot] uk
[[About FREAD]]
[[Download (for 32-bit linux)|./download/FREAD-3.0.1-linux32.tar.gz]]
[[Download (for 64-bit linux)|./download/FREAD-3.0.1-linux64.tar.gz]]

[[Download (for 32-bit Windows XP)|./download/FREAD-3.0.1-windowsXP.zip]]

They were compiled using GNU gcc version 4.3.2 (Linux kernel 2.6).

Each version must contain:
*README
*BUILD
**Database building file
*FREAD
**Actual running file
*allmat.dat
**Environment Specific Substitution Score Tables^^1^^
*moult.dat
**~Samudrala-Moult energy data file^^2^^

#J. Shi, T. Blundell and K. Mizuguchi (2001), FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties, J. Mol. Biol., 310, 243-257
#R Samudrala and J. Moult (1998), An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction1, J. Mol. Biol., 275, 895-916
!Database Build
The FREAD database contains the information of Cα separations.

There are a few things you should be careful of.
*The PDB files and the database ''@@must@@'' be located in the same folder.
*Multi-chain PDB structures ''@@must@@'' be separated chain by chain.
*The PDB file ''@@must@@'' have 4 PDB code letters + 1 chain identifier. For example,
**{{{2v9tB.pdb}}} or {{{2v9tB.atm}}}
I included a simple [[python code|./FREAD-Database.py]].
{{{$ ./FREAD-database.py 2v9t.pdb}}}
The code cleans and breaks a PDB file into chains (if a structure was determined by NMR, the code will take only the first model).

!Options
There are several options you can set.

!!! Compulsory Options
*''-f'': Query structure
*''-m'': Log file
*''-l'': Loop length
*''-s'': Starting residue of the query loop
*''-b'': Base directory. In the base directory, there must be "allmat.dat", "moult.mat" and PDB structure files.
**If you do not specify a database you use for prediction, the database directory is the base directory by default.

!!! Optionals
*''-d'': Database file. The database file should be located in the base directory. If you do not specify this option, FREAD tries to use "THELIST.db" file in the base directory.
*''-C'': Environment specific substitution score cut-off. 25 by default.
*''-R'': ~FREAD-R option. If you specify this option, FREAD tries to relax anchor restrictions for 3 cycles and find more fragment candidates.
*''-O'': Output file control. If you specify this option, FREAD does not create predictions in the PDB style.
*''-r'': RMSD calculation. If you do not specify this option, FREAD does not calculate local and global loops ~RMSDs and the ~RMSDs do not appear in log files.
*''-q'': Sequence file. If a query structure does not have coordinates, but only sequence, this option must be used. The sequence file should have a MODELLER alignment style.
{{{
>P1;2v9tB
structure:2v9t: 269 :B: 478 :B:unknown:unknown:-1:-1
GSLHCPAACTCSNNIVDCRGKGLTEIPTNLPETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISE
LAPDAFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNKL
QTIAKGTFSPLRAIQTMHLAQNPFICDCHLKWLADYLHTNPIETSGARCTSPRRLANKRIGQIKSKKFRC
*
}}}

!Example

{{{
$ ./FREAD -f../query/2v9tB.pdb -l18 -s286 -r -q./query/2v9tB.ali -d./FREAD_DB/temp.db -b./FREAD_DB/ -C30 -m2v9tB_18_286.log
****************************************************
* FREAD - Frangment search algorithm               *
*                                                  *
* Originally written by Dr Charlotte Deane in 2000 *
* Revised and modified by Yoonjoo Choi in 2009     *
****************************************************

Loop Region Sequence: CRGKGLTEIPTNLPETIT




The FREAD Database you are using is ./FREAD_DB/temp.db
The environment specific substitution score cut-off is 30
Reading database...
19 fragments are found!
Samudrala-Moult function is being calculated...
Done! You have 19 fragments.

The log file is 2v9tB_18_286.log
}}}

!Log File

The results are sorted in terms of anchor matches.

|!Fragment ([code][chain]_[length]_[start residue]) |! Anchor RMSD |! ~Samudrala-Moult energy |! Start residue |! Environment substitution score |! Local loop RMSD |! Global loop RMSD|
|2v9tA_18_286.pdb   |    0.000   |   -1.310   |   286  |   142   |   0.000    |   0.000|
|1xkuB_18_107.pdb  |     0.103   |   -0.928  |    107  |    40  |    0.756   |    1.105|
|>|>|>|>|>|>| .................................................................................. |
|Log file entry|c

{{{
2v9tA_18_286.pdb       0.000      -1.310      286     142      0.000       0.000
1xkuB_18_107.pdb       0.103      -0.928      107      40      0.756       1.105
 3e6jA_18_35.pdb       0.131      -0.911       35      41      0.713       1.854
 1p9aA_18_17.pdb       0.136      -0.736       17      49      1.123       1.510
 2o6qA_18_45.pdb       0.137      -0.860       45      64      0.716       1.527
 2o6sA_18_37.pdb       0.146      -0.785       37      48      0.758       1.504
 1xkuA_18_38.pdb       0.157      -0.920       38      38      0.287       0.594
3bz5A_18_291.pdb       0.160      -0.390      291      31      1.920       2.456
3bz5A_18_228.pdb       0.171      -0.229      228      39      1.997       2.969
 1ziwA_18_37.pdb       0.180      -0.727       37      68      0.835       1.083
3bz5A_18_355.pdb       0.185       0.030      355      46      1.824       2.771
 2z62A_18_40.pdb       0.191      -0.485       40      36      1.117       1.554
 2o6rA_18_37.pdb       0.192      -1.163       37      65      0.730       1.463
 2z66A_18_37.pdb       0.193      -0.697       37      64      0.760       1.602
3bz5A_18_185.pdb       0.193      -0.265      185      59      1.840       2.270
1xkuA_18_178.pdb       0.230       0.067      178      33      0.790       1.559
3bz5G_18_164.pdb       0.252      -0.178      164      31      1.880       2.397
 2z81A_18_38.pdb       0.308      -0.784       38      47      0.987       1.668
 3cigA_18_37.pdb       0.537       1.742       37      60      1.021       2.596
}}}
!!Loop Definition

!!!Native Structures

[[Test set download|.//loop_set.soluble]]

The loops in this test set were extracted from high-resolution X-ray structures of non-membrane proteins using PISCES^^1^^.
#Sequence identity percentage ≤ 90%
#Resolution ≤ 2Å
#R-factor ≤ 0.2
The PDB chains were cleaned and annotated using JOY^^2^^.
#A loop structure was defined as a region between two secondary structures that are at least 3 residues in length. ^^3^^
#Short loops were discarded (less than 4 residues)
#Pairwise sequence alignments of identical length loops were performed.
##If the sequence identity between two loops was greater than 40%^^4^^, the sequence with the lower B-factor was kept while the other was discarded.

!!!Entry

|!PDB code |! PDB chain |! Loop length |! Start residue |! End residue |! SSE of ~N-Terminal |! SSE of ~C-Terminal|!B-factor|!Hydrophobicity|!Sequence|
| 2r8o | A | 4 | 407 | 410 | B | H |  4.336 | -0.500 | YGVR |
| 3c1q | A | 4 |  95 |  98 | H | H  | 8.078  | -2.925 | QSEK |
| 3cls | D | 4 | 135 | 138 | B | B  | 6.510 | -3.050 | YNQK |
|>|>|>|>|>|>|>|>|>| .................................................................................. |
*SSE: Secondary Structure Element. "H": α helix, "B": β strand
*B-factor: Average thermal factor of a loop
*Hydrophobicity: Average hydrophobicity of a loop (~Kyte-Doolittle hydrophobicity scale)

#K. Wang, R. Dunbrack, Jr. (2003), PISCES: a protein sequence culling server, Bioinformatics, 12, 1589-1591
#K. Mizuguchi, C. Deane, T. Blundell, M. Johnson and J. Overington (1998), JOY: protein sequence-structure representation and analysis, Bioinformatics, 14, 617-623
#L. Donate, L. Ruffino and T. Blundell (1996), Conformational analysis and clustering of short and medium size loops connecting regular secondary structure: A database for modeling and prediction, Protein Sci., 5, 2600-2616
#N. ~Fernandez-Fuentes and A. Fiser (2006), Saturating representation of loop conformational fragments in structure databanks, BMC Structural Biology, 6, 15-26

!!!CASP Model Structures

[[CASP7 loop definition download|./CASP7/loop_definition.CASP7]]
[[CASP7 models download|./CASP7/CASP7.bestmodels.tar.gz]]
[[CASP8 loop definition download|./CASP8/loop_definition.CASP8]]
[[CASP8 models download|./CASP8/CASP8.bestmodels.tar.gz]]

The best models according to the LGA score were selected. As we do not have the target template alignment that produced the CASP models, we assume that the "loop" regions are those which are predicted poorly. If the distance between Cα atoms of a common residue in a model and its native structure is bigger than 5Å after global superposition, the region is defined as a "loop".

Note that the model structures above are not the same as the coordinate files in the CASP webpage. The residues of some structures were cut and shifted.
[[About FREAD]]
[[Download]]
[[How to use?]]
[[Loop Test Set]]
[[Trouble Shooting]]
[[Contact]]
a database search loop structure prediction algorithm
FREAD
!"Segmentation Fault"

The error may occur because of your stacksize. You can simply resolve this problem by changing your stacksize.

First, check your shell.

{{{
$ ps | grep `echo $$` | awk '{ print $4 }'
}}}

!! Bash

{{{
$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 257816
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 10000
cpu time               (seconds, -t) unlimited
max user processes              (-u) 1024
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited
}}}

You may as well change your stacksize to "unlimited".

{{{
$ ulimit -Ss unlimited
$ ulimit -Ss
unlimited
}}}

!! Cshell

{{{
$ limit
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    10000 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      1024 
}}}

You may as well change your stacksize to "unlimited".

{{{
$ limit stacksize unlimited
$ limit
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    unlimited
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      1024 
}}}

!!
''If you encounter any other problems, please email
#choi [at] stats [dot] ox [dot] ac [dot] uk
#yoonjoo.choi [at] stx [dot] ox [dot] ac [dot] uk''
Yoonjoo Choi is a DPhil student in statistics at Oxford university.

I am currently working on protein loop structure prediction.