jianlin-cheng / dfold Goto Github PK

git clone https://github.com/jianlin-cheng/DFOLD.git

(If fail, try username) git clone https://[email protected]/jianlin-cheng/DFOLD.git

cd DFOLD

a. edit setup_database.pl
    (i) Manually create folder for database (i.e., /data/commons/DFOLD_db_tools/)
    (ii) Set the path of variable '$DFOLD_db_tools_dir' for DFOLD databases and tools (i.e., /data/commons/DFOLD_db_tools/).

b. perl setup_database.pl

a. edit configure.pl

b. set the path of variable '$DFOLD_db_tools_dir' for DFOLD databases and tools (i.e., /data/commons/DFOLD_db_tools/).

c. save configure.pl

perl configure.pl

cd examples

sh T0_run_DFOLD-1ALY-A.sh

sh T0_run_DFOLD-1AYO-B.sh

sh T0_run_DFOLD-1BYR-A.sh

sh T0_run_DFOLD-1CCW-C.sh

sh T0_run_DFOLD-1G5T-A.sh



Output examples:
Job successfully completed!
Results: /data/jh7x3/DFOLD/test_out/1ALY-A/stage2/1ALY-A_model1.pd

Validating the results

/data/jh7x3/DFOLD/tools/TMscore  /data/jh7x3/DFOLD/test_out/1ALY-A/stage2/1ALY-A_model1.pdb  /data/jh7x3/DFOLD/installation/benchmark/native_structure/1ALY-A.pdb

 *****************************************************************************
 *                                 TM-SCORE                                  *
 * A scoring function to assess the quality of protein structure predictions *
 * Based on statistics:                                                      *
 *       0.0 < TM-score < 0.17, Random predictions                           *
 *       0.4 < TM-score < 1.00, Meaningful predictions                       *
 * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710     *
 * For comments, please email to: [email protected]                              *
 *****************************************************************************

Structure1: /data/jh7x  Length=  146
Structure2: /data/jh7x  Length=  146 (by which all scores are normalized)
Number of residues in common=  146
RMSD of  the common residues=    0.337

TM-score    = 0.9945  (d0= 4.50, TM10= 0.9945)
MaxSub-score= 0.9911  (d0= 3.50)
GDT-TS-score= 0.9983 %(d<1)=0.9932 %(d<2)=1.0000 %(d<4)=1.0000 %(d<8)=1.0000
GDT-HA-score= 0.9795 %(d<0.5)=0.9247 %(d<1)=0.9932 %(d<2)=1.0000 %(d<4)=1.0000

 -------- rotation matrix to rotate Chain-1 to Chain-2 ------
 i          t(i)         u(i,1)         u(i,2)         u(i,3)
 1    -12.4677703609  -0.0762551404   0.2831125431   0.9560504388
 2     -2.3407693147   0.0043722315  -0.9587381018   0.2842571649
 3      1.7943000641   0.9970787517   0.0258561439   0.0718708750

Superposition in the TM-score: Length(d<5.0)=146  RMSD=  0.34
(":" denotes the residue pairs of distance < 5.0 Angstrom)
GDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
GDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL
12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456

   Usage:
   $ sh bin/run_DFOLD.sh <target id> <file name>.fasta <path of predicted secondary structure> <path of distance> <output folder>

   Example:
   $ sh bin/run_DFOLD.sh 1ALY-A  /data/jh7x3/DFOLD/examples/1ALY-A.fasta  /data/jh7x3/DFOLD/examples/1ALY-A.ss  /data/jh7x3/DFOLD/examples/1ALY-A.dist.rr  /data/jh7x3/DFOLD/test_out/1ALY-A_out

*** run DFOLD on real 

perl scripts/P1_run_DFOLD_batch.pl /data/jh7x3/DFOLD/installation/benchmark/original_seq/  /data/jh7x3/DFOLD/installation/benchmark/seq_secondary_structure_by_SCRATCH/ /data/jh7x3/DFOLD/installation/benchmark/native_structure /data/jh7x3/DFOLD/installation/benchmark/true_distance_cb/  /data/jh7x3/DFOLD/test_out/DFOLD_trueRes_folding

cd /data/jh7x3/DFOLD/test_out/DFOLD_trueRes_folding
cp */stage2/*_model1.pdb summary/


perl /data/jh7x3/DFOLD/scripts/P1_evaluate_DFOLD_batch.pl /data/jh7x3/GFOLD/test_out/DFOLD_trueRes_folding/summary /data/jh7x3/DFOLD/installation/benchmark/native_structure/