DOCKovalent linker design tutoral: Difference between revisions

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reaction2:
reaction2:
  python step2-reaction-SF-meta.py scaffold.ism
  python step2-reaction-SF-meta.py scaffold.ism
                         input file: scaffold.ism is the primary products without the SF
                         input file: scaffold.ism is the primary product without the SF
                         output file: final_scaffold1.smi
                         output file: final_scaffold1.smi


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The no_double_out.ism was used to generate db2 file for covalent docking
The no_double_out.ism was used to generate db2 file for covalent docking
log into gimel
log into gimel
  setenv DOCKBASE /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
  setenv DOCKBASE /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
  setenv DOCKBASE /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
  setenv DOCKBASE /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
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  bash step0_prepare_build_system.sh  5K9I-B-X44
  bash step0_prepare_build_system.sh  5K9I-B-X44
In the window of chimera, select all of the 27 lysine rotamers and click the button of OK. Reselect all the lysine rotamers in the PDB structure, and the save to PDB format LYS-5K9I-B-X44.pdb
In the window of chimera, select all of the 27 lysine rotamers and click the button of OK. Reselect all the lysine rotamers in the PDB structure, and the save to PDB format LYS-5K9I-B-X44.pdb
Then, to generate all 28 structure folds, and then automatically calculate the steric clash with nearby residues, and select the rotamer with no steric clashes. This scripts will also calculate the nearest atom of in the compound to the lysine NZ atom
Then, to generate all 28 structure folds, and then automatically calculate the steric clash with nearby residues, and select the rotamer with no steric clashes. This script will also calculate the nearest atom of in the compound to the lysine NZ atom
  bash step1_run_build_system.sh 5K9I-B-X44  
  bash step1_run_build_system.sh 5K9I-B-X44  
  results
  results
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==Step 3 modify the INDOCK parameters for saving multiple poses ==
==Step 3 modify the INDOCK parameters for saving multiple poses ==


cd 3-modify-the-INDOCK-parameters
cd 3-modify-the-INDOCK-parameters
change the default parameters for covalent docking
change the default parameters for covalent docking


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==Step 4  run the covalent docking in gimel==
==Step 4  run the covalent docking in gimel==
cd 4-run-the-covalent-docking
cd 4-run-the-covalent-docking


contain a pharmacophore filter ( exclusion criteria that ligands should form hydrogen bonds with the kinase hinge region, and the shared pyrimidine 3-aminopyrazole scaffold should be within 2 Å compared to the crystal conformation)
contain a pharmacophore filter ( exclusion criteria that ligands should form hydrogen bonds with the kinase hinge region, and the shared pyrimidine 3-aminopyrazole scaffold should be within 2 Å compared to the crystal conformation)


Prepare 1)the modified INDOCK file INDOCK.bump1000000000000.pose1000.20.5.5
Prepare  
        2)the gate residue file (define the two residue in the SRC kinase domain MET341  VAL399)
1)the modified INDOCK file INDOCK.bump1000000000000.pose1000.20.5.5
2)the gate residue file (define the two residue in the SRC kinase domain MET341  VAL399)
Input file :
Input file :
        1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
        2) the ligand library folder name (lib1)
2) the ligand library folder name (lib1)
        3) the linker name list (lib1.list)
3) the linker name list (lib1.list)
bash /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_cys_wiki-tutorial/4-run-the-covalent-docking/qsub_multipe_jobs structure-list lib1  lib1.list
  bash /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_cys_wiki-tutorial/4-run-the-covalent-docking/qsub_multipe_jobs structure-list lib1  lib1.list
 
==Step 5 Analysis and combine the top1 pose from different structures==


==Step 5 Analysis and combine the top1 poses from different structures==
  cd 5-Analysis-and-combine-the-top1-poses-from-different-structures
cd 5-Analysis-and-combine-the-top1-poses-from-different-structures
after the covalent docking, analyze the docking results
after the covalent docking, analyze the docking results
bash step1_extract_the_best_score.sh  structure-list lib1  lib1.list
 
  bash step1_extract_the_best_score.sh  structure-list lib1  lib1.list
       Inputfile :
       Inputfile :
       1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
       1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
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combine the docking results
combine the docking results
         bash step3_combine-best-energy.sh structure-list lib1
         bash step3_combine-best-energy.sh structure-list lib1
         Input file :
         Input file :
         1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
         1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
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         2)submit.new.aura-A-X63.list.dat                the name of structure file and linker
         2)submit.new.aura-A-X63.list.dat                the name of structure file and linker


==Step 6 Run the minimization and MMGBSA rescoreing==
==Step 6 Run the minimization and MM/GBSA rescoreing==
cd 6-Run-the-minimization-and-MMGBSA-rescoring
 
  cd 6-Run-the-minimization-and-MMGBSA-rescoring
First, check the protonation state of each linker after when using the chimera to add hydrogen
First, check the protonation state of each linker after when using the chimera to add hydrogen
second, the different H position of linkers will result in the different labelling number of the attached NH of lysine residue
second, the different H position of linkers will result in the different labelling number of the attached NH of lysine residue
prepare the list for each linker containing these two informations in XO44.charge.list file (default:xabs    1      1)
prepare the list for each linker containing two informations in XO44.charge.list file (default:xabs    1      1)
 


bash step7_fix_prolem_resubmit_MMPBSA.minimization.sh INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB
  bash step7_fix_prolem_resubmit_MMPBSA.minimization.sh INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB
INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB is the folder for runing minimization
INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB is the folder for runing minimization


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extract the scoring number for each linker
extract the scoring number for each linker
bash step6_resubmit.extract_GBscore.sh list
  bash step6_resubmit.extract_GBscore.sh list
the list contains (INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB)
the list contains (INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB)


==Step 7 analyze the final pose by chimera==
==Step 7 analyze the final pose by chimera==
cd 7-analyze-the-final-pose-by-chimera
  cd 7-analyze-the-final-pose-by-chimera
first sort the linker according to the MMGBSA score
first sort the linker according to the MMGBSA score
cat MMGBSA.list | sort -nk 2 >sort.MMGBSA.list
  cat MMGBSA.list | sort -nk 2 >sort.MMGBSA.list


   1-extract the pose without the protein
   1-extract the pose without the protein
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using the chimera to visualize these poses and select the final linker (save to PDB file)
using the chimera to visualize these poses and select the final linker (save to PDB file)
   save the linker viewdock state: P
   save the linker viewdock state: P
   perl step0-filter_by_the_chimera.pl pdb  to extract the final poses
   perl step0-filter_by_the_chimera.pl pdb  to extract the final poses

Latest revision as of 00:21, 6 April 2018

This was written on April 4, 2018.

This tutorial is for designing linkers for a covalent inhibitor and is supplement the work in preparation (Wan et al 2018).


These file are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki-tutorial


Step 1. Custom Ligand and Library Generation

1/Custom Ligand / Library Generation

cd 1-Custom-Ligand-Library-Generation

For meta-SF library building

reaction1: scaffod.smi is the smile of the scaffold for reaction 817.zinc.list.smi is the smile of collect 817 different diamine linkers

python step1-reaction-amines-Br.py scaffod.smi 817.zinc.list.smi
                      

reaction2:

python step2-reaction-SF-meta.py scaffold.ism
                       input file: scaffold.ism is the primary product without the SF
                       output file: final_scaffold1.smi

reaction3: remove the doubles

python step3-remove_doubles.py final_scaffold1.smi
                       inputfile:final_scaffold1.smi
                       outputfile: no_doubles_out.ism

The no_double_out.ism was used to generate db2 file for covalent docking

log into gimel
setenv DOCKBASE /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
setenv DOCKBASE /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
/nfs/soft/tools/utils/qsub-slice/qsub-mr-meta -tc 50 --map-instance-script "/nfs/soft/tools/utils/qsub-slice/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT -l 1 no_doubles_out.ism $DOCKBASE/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent

Step 2 Protein preparation (different lysine rotamers)

2/Protein preparation (different lysine rotamers)

cd 2-Protein-preparation-different-lysine-rotamers

find the modification lys number in the PDB

echo "5K9I-B-X44      B       295">>lys.list
bash step0_prepare_build_system.sh  5K9I-B-X44

In the window of chimera, select all of the 27 lysine rotamers and click the button of OK. Reselect all the lysine rotamers in the PDB structure, and the save to PDB format LYS-5K9I-B-X44.pdb Then, to generate all 28 structure folds, and then automatically calculate the steric clash with nearby residues, and select the rotamer with no steric clashes. This script will also calculate the nearest atom of in the compound to the lysine NZ atom

bash step1_run_build_system.sh 5K9I-B-X44 
results
5K9E-B-X44      SBH     2.038
5K9B-B-X44      SBH     2.321
5K9I-B-X44      OBI     2.949
5K9L-B-X44      SBH     4.683
5K9R-B-X44      OBI     4.925

Each folder contains rec.pdb and xtal-lig.pdb

For each folder

bash step1_DOCKINV.blastermaster.sh 5K9I-B-X44 box_margin(10) 1(covalent docking)

box_margin is defined from the center of the xtal-lig.pdb file

Step 3 modify the INDOCK parameters for saving multiple poses

cd 3-modify-the-INDOCK-parameters

change the default parameters for covalent docking

 bump_maximum                  100
 bump_rigid                    100
 number_save                   1000
 number_write                  1000
 molecules_maximum             100000
 bond_len                      1.61
 bond_ang1                     121.02
 bond_ang2                     107.36
 len_range                     0.0
 len_step                      0.1
 ang1_range                    20.0
 ang2_range                    20.0
 ang1_step                     5
 ang2_step                     5
 check_clashes                 no
 per_atom_scores               yes

Step 4 run the covalent docking in gimel

cd 4-run-the-covalent-docking

contain a pharmacophore filter ( exclusion criteria that ligands should form hydrogen bonds with the kinase hinge region, and the shared pyrimidine 3-aminopyrazole scaffold should be within 2 Å compared to the crystal conformation)

Prepare

1)the modified INDOCK file INDOCK.bump1000000000000.pose1000.20.5.5
2)the gate residue file (define the two residue in the SRC kinase domain MET341  VAL399)

Input file :

1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
2) the ligand library folder name (lib1)
3) the linker name list (lib1.list)
 bash /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_cys_wiki-tutorial/4-run-the-covalent-docking/qsub_multipe_jobs structure-list lib1  lib1.list

Step 5 Analysis and combine the top1 pose from different structures

 cd 5-Analysis-and-combine-the-top1-poses-from-different-structures

after the covalent docking, analyze the docking results

 bash step1_extract_the_best_score.sh  structure-list lib1  lib1.list
      Inputfile :
      1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
      2) the ligand library folder name (lib1)
      3) the linker name list (lib1.list)

combine the docking results

       bash step3_combine-best-energy.sh structure-list lib1
       Input file :
       1) the list different structure folders (5K9A-B-X44,5K9A-C-X44)
       2) the ligand library folder name (lib1)
       Output file:
       1)sort.final.combine-new.aura-A-X63.list.dat    rank all of the top1 pose for each linker
       2)submit.new.aura-A-X63.list.dat                the name of structure file and linker

Step 6 Run the minimization and MM/GBSA rescoreing

 cd 6-Run-the-minimization-and-MMGBSA-rescoring

First, check the protonation state of each linker after when using the chimera to add hydrogen second, the different H position of linkers will result in the different labelling number of the attached NH of lysine residue prepare the list for each linker containing two informations in XO44.charge.list file (default:xabs 1 1)

 bash step7_fix_prolem_resubmit_MMPBSA.minimization.sh INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB

INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB is the folder for runing minimization

after minimization, then run the AMBER MMGBSA rescoring bash step10_fix_prolem_resubmit_MMPBSA_score.sh INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB

extract the scoring number for each linker

 bash step6_resubmit.extract_GBscore.sh list

the list contains (INDOCK.bump1000000000000.pose1000.20.5.5-xo4E-A-X44-X44-meta-xaaa-1-mini_end_GB)

Step 7 analyze the final pose by chimera

 cd 7-analyze-the-final-pose-by-chimera

first sort the linker according to the MMGBSA score

 cat MMGBSA.list | sort -nk 2 >sort.MMGBSA.list
 1-extract the pose without the protein
 perl fix-step3_extract_best_score_combinepdb_after_minimize.pl sort.MMGBSA.list
 2-extract the pose with the protein
 perl fix-step4_extract_best_score_combinepdb_after_minimize_with_rec.pl sort.MMGBSA.list

using the chimera to visualize these poses and select the final linker (save to PDB file)

 save the linker viewdock state: P
 perl step0-filter_by_the_chimera.pl pdb  to extract the final poses