BILBODOCK

BILBODOCK – Structure prediction of protein and protein/DNA complexes constrained by solution scattering data and protein docking

Written by: Michal Hammel & Martin Pelikan & Ken Frankel

Hardware platforms: in the moment on our LINUX - cluster only

ask MH for acces ( mhammel@lbl.gov )

Short user instructions

The program BILBODOCK allows determination of three-dimensional structure of proteins or protein/DNA assemblies based on docking prediction. Protein crystal structures are generally monomeric, however biologically active samples and proteins in solution often form multimers. Docking searches are used to predict the interface of dimers and higher-order multimers. We start with a known structures of single protein. The docking search returns a set of candidate structures that are subsequently validated by fit of the theoretical SAXS profiles to the experimental data. Three separate strategies you may try.

1. EMAP - performs a global search of the Receptor (protein 1) and Ligand (protein2) binding sites using a modify EMAP (Modeling macromolecular assemblies with map objects) docking approach described by CHARMM developer. In this approach a rigid domain is defined to represent a map at the position and orientation of an atomic structure containing charge, electro-static field and vdw core distribution and can be moved around as a molecular structure. These molecular maps provide a convenient way to evaluate interactions between map objects through map energies (dock.trj) and the structure of macromolecular assemblies can be modeled through docking approach. In our scenario molecular map obtained for Receptor atomic structure is assigned as fixed and the Ligand map calculated for protein or DNA atomic models are allowed to move and docked to the Receptor map. The grid-threading Monte Carlo is used to sample an infinity orientation of Ligand over Receptor surface followed by the energy-based docking-search. 1216 different docking sites are validated by subsequent calculations of the theoretical scattering profiles. This strategy produces only structures with proper contacts between the Receptor and Ligand and allowed us to find complex which best match the experimental scattering data (crysol.out). The figure show the validation of all 1216 modeled assemblies by plotting the goodness of fit (^)vs. R_G

Note: this approach is fast and allowed dock DNA also.

2. ZDOCK - protein docking ( http://zlab.bu.edu/zdock/ ). ZDOCK uses a fast Fourier transform to search all possible binding modes for the proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics (zdock.out). Take the top complex predictions and validate them by by subsequent calculations of the theoretical scattering profiles (crysol.out).

Note: this approach is SLOWER and DO NOT allowed dock DNA also.

3. MDOCK – is the same approach as ZDOCK, except the symmetry constrain in the interface predictions.

Note: possibility to building protein homo-multimers

How to start?

> ssh sibyls@bl1231.als.lbl.gov

> ssh crush

> cd # to your directory where the initial structures (xxx.pdb) and experimental data (xxx.dat) are located

sibyls@crush:pkh1/dock 21% bilbodock

*********************************************************
****************** BILBODOCK version 1.1 ****************
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***writen by Michal & Martin & Ken release 07/2008 ******
*****should help to everybody who want to used **********
***********docking conformational sampling and EOM ******
************* rigid body modeling ***********************
***************of protein complexes *********************
*************** or dna/protein **************************
*********************************************************
*********************************************************
*********************************************************
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1 - Docking DNA/protein or protein/protein using EMAP procedure (FAST!!!)

2 - Docking protein/protein using ZDOCK

3 - Docking protein multimers using MDOCK

1 ◄┘

Do you want enseble optimization (EOM) <N> ◄┘

# BILBODOCK can performed ensemble optimization method using saved *fit files. The scattering curves from all the prediction - structures (saved in ../fit/ directory).
BILBOMD select ensemble with 2, 3, 4 and 5 structure with following output

Enter the experimental DAT file

pkh1.dat ◄┘

qmax ? <0.3> ◄┘

Do you want specify CRYSOL parameter? <N> ◄┘

Enter Receptor ***.pdb! # input your Receptor pdb

pk.pdb ◄┘

ATOM      1 N   GLY     1      17.774 -54.525 14.682 1.00 0.00
ATOM      2 CA GLY     1      19.072 -54.576 14.058 1.00 0.00
ATOM      3 C   GLY     1      18.912 -54.049 12.717 1.00 0.00
ATOM      4 O   GLY     1      19.846 -54.018 11.974 1.00 0.00
..
..
..

Enter Receptor ***.pdb! # input your Ligand pdb

h1.pdb ◄┘

ATOM      1 N   ASN     1     -61.067 21.000 -8.354 1.00 0.00
ATOM      2 CA ASN     1     -60.707 19.703 -7.767 1.00 0.00
ATOM      3 CB ASN     1     -60.384 19.809 -6.267 1.00 0.00
..
..
..

# Your initial structure will be clean up from REMARKS, HETATOM etc.. and rename, starting by #1

# BILBODOCK start and perform the operations 1,2 or 3

BILBODOCK OUTPUT

1. EMAP

dock.trj > validation of all conformations based on the interface ( #, 1, Total Energy, , , , ,)

the lower energy the better interface

crysol.out > validation of all conformations ( filename , Rg, χ²)

dock_all.pdb > all conformation in CA representation

../fit/ > directory with all complex structures and crysol fits

2. ZDOCK

zdock.out > validation of all conformations based on the interface ( trans_rot_matric, total score)

the higher score the better interface

crysol.out > validation of all conformations (#filename , Rg, χ²)

../Predictions/ > directory with all complex structures and crysol_fits

3. MDOCK

mzdock.out > validation of all conformations based on the interface ( trans_rot_matric, total score)

the higher score the better interface

crysol.out > validation of all conformations (#filename , Rg, χ²)

../Predictions/ > directory with all complex structures and crysol_fits

3. EOM

<filname>ga*_list1.pdb > multiconformational model in pdb format
avg_optimal_ga*.dat > multiconformational fit to the experimental data

ga*list.sta > conformational validation molecule/ RMSD/ RG /External_Distance /Internal_Dist.