Requires Python 3.x, absl-py and numpy
- sc from ccp4 (http://www.ccp4.ac.uk/) [executable_name: sc]
- delphi v.6.2 (http://compbio.clemson.edu/delphi) [executable_name: delphi95]
- Rosetta (https://www.rosettacommons.org/software/)
- ProQ2 (https://github.com/bjornwallner/ProQ_scripts/)
- needle from EMBOS (http://emboss.sourceforge.net/download/)
$ git clone https://github.com/bjornwallner/ProQDock
$ cd ProQDock
$ ./compileF # Assumes you have gfortran installededit the flagfile and change the fullpaths for the following fields according to your system and save it as myflagfile:
--sc_path=/software/presto/software/CCP4/7.1.016-foss-2019b-SHELX-ARP-8.0-1/ccp4-7.1/bin/
--delphi_path=/proj/wallner/users/x_bjowa/local/DelPhi_Linux_SP_F95/
--rosetta=/proj/wallner/apps/rosetta/Rosetta/main/
--svm_path=/proj/wallner/users/x_bjowa/local/svm_light_linux64/
--proqpath=/proj/wallner/users/x_bjowa/github/ProQ_scripts/bin/ 1. The coordinate (PDB) file for the model
2. The full-length target sequence (in FASTA format)
- The model must be either the full-length sequence or subset of the target sequence
- i.e., Any and all sub-sequence present in the model must be present in the tareget
- PDB file MUST contain corrdinates of geometrically fixed Hydrogen atoms
- preferably fixed by REDUCE v.2 or atleast compatible with the REDUCE format (http://kinemage.biochem.duke.edu/downloads/software/reduce/)
The full length (FASTA) target sequence (one letter amino acid code followed by a header starting with >) should be prepared and provided alongside the coordinate (PDB) file for the model.
You can generate the fasta sequence by using:
$ EXEC/pdb2fasta.pl <input.pdb> > input.pdb.fasta$ ./run_ProQDock.py <model.PDB> <full-length.fasta> --flagfile myflagfilewhere,
- model.pdb: The input pdb (coordinate file in Brrokheaven format; http://www.ccp4.ac.uk/html/procheck_man/manappb.html) file
- full-length.fasta: The full-length fasta sequence of the target
If you intend to Run ProQDock for a list of PDB files (models) corresponding to the same target sequence, then, SKIP repeating the profile generation step more than once, by providing a [consistent basename] for the fasta file.
$ ./run_ProQDock.py <model.PDB> --AF --flagfile myflagfileThe following bash script which runs on a set of (example) models kept at ./EXAMPLE_CASE_STUDY/
$ ./runex.bashExample Output for a single PDB file:
$ ./run_ProQDock.py ./TESTPDBS/1u07.pdb ./TEMP/1u07.pdb.fasta --flagfile flagfile .... .... ..
.n~8888888nx .xH888888Hx. < .z@8"`
.d`` .u . u. :88>'8888888888: .H8888888888888: u. !@88E
@8Ne. .u .d88B :@8c ...ue888b :8888 "*888888888k 888*"""?""*88888X ...ue888b . '888E u
%8888:u@88N ="8888f8888r 888R Y888r '88888. "8> 'f d8x. ^%88k 888R Y888r .udR88N 888E u@8NL
`888I 888. 4888>'88" 888R I888> ?88888 'X '> <88888X '?8 888R I888> <888'888k 888E`"88*"
888I 888I 4888> ' 888R I888> ? %888! ! `:..:`888888> 8> 888R I888> 9888 'Y" 888E .dN.
888I 888I 4888> 888R I888> ".:88" ! `"*88 X 888R I888> 9888 888E~8888
uW888L 888' .d888L .+ u8888cJ888 xHH8Hx. .X : .xHHhx.." ! u8888cJ888 9888 888E '888&
'*88888Nu88P ^"8888*" "*888*P" :888888888hx....x\8..X X88888888hx. ..! "*888*P" ?8888u../ 888E 9888.
~ '88888F` "Y" 'Y" :~ `"8888888888!`'8888 ! "*888888888" 'Y" "8888P' '"888*" 4888"
888 ^ `""*8*""` "*" ^"***"` "P' "" ""
*8E
'8>
"
=================================================================================================================================
Feature Range Direction Description Feature_Type Stability Native_values (DB3)
---------------------------------------------------------------------------------------------------------------------------------
EC: [-1,1] Positive Electrostatic balance at the interface Interface Variable 0.20 (+/-0.38)
Sc: [-1,1] Positive Geometric / Steric fit at the interface Interface Stable 0.68 (+/-0.17)
rGb: [-1,1] Positive Distribution of hydrophobicity with respect to burial All_Atom Stable 0.06 (+/-0.02)
Ld: [0, 1] Ambiguous Link (packing) densely at the interface Interface Stable 0.15 (+/-0.17)
nBSA: [0, 1] Ambiguous Size of the interface relative to the whole complex Interface Variable 0.07 (+/-0.05)
Fintres: [0, 1] Ambiguous Size of the interface relative to the whole complex Interface Variable 0.19 (+/-0.13)
CPscore: [0, 1] Positive inter-residue contacts preference Interface Variable 0.35 (+/-0.17)
CPM: [0, 1] Positive Likelihood of (Sc,EC) given nBSA compared to native Interface Variable 0.80 (+/-0.18)
rTs: [0, 1] Negative Energetic Stability of the whole molecule All_Atom Stable 0.22 (+/-0.21)
Isc: [0, 1] Negative Binding energy Interface Variable 0.20 (+/-0.33)
Erep: [0, 1] Negative Unfavourable Energy due to atomic Clashes All_Atom Stable 0.41 (+/-0.15)
Etmr: [0, 1] Negative Energetic Stability without condiderating clashes All_Atom Stable 0.28 (+/-0.16)
ProQ2: [0, 1] Positive Overall Structural Quality All_Atom Variable 0.80 (+/-0.12)
---------------------------------------------------------------------------------------------------------------------------------
ProQDock [0, 1] Positive The predicted DockQ score, Basu and Wallner, 2016, https://doi.org/10.1371/journal.pone.0161879
DockQ Statistics on CAPRI data:
0 < DockQ < 0.23 - Incorrect
0.23 <= DockQ < 0.49 - Acceptable quality
0.49 <= DockQ < 0.80 - Medium quality
DockQ >= 0.80 - High quality
=================================================================================================================================
EC=0.259
Sc=0.495
rGb=0.028
Ld=0.102
nBSA=0.054
Fintres=0.193
CPscore=0.161
CPM=0.422
Isc=0.923
rTs=0.898
Eatr=0.085
Erep=0.549
Etmr=0.873
ProQ2=0.794
==========================
ProQDock=0.266
Finding correct protein–protein docking models using ProQDock
Sankar Basu and Björn Wallner*
Bioinformatics (2016) 32 (12): i262-i270.
doi: 10.1093/bioinformatics/btw257
The article is avialable online here: http://bioinformatics.oxfordjournals.org/content/32/12/i262.abstract