DR-SIP: Distance Restraints- and Cyclic Symmetry-Imposed Packing

DR-SIP contains tools and molecular docking protocols for predicting the quaternary structures of homo-oligomeric transmembrane proteins (HoTPs) by assuming the complex is cyclic (C_n) symmetric and filtering docking poses with experimentally measured distance restraints between the monomers in the complex.

The DR-SIP package contains 4 Python modules:

1. drsip: Implements the molecular docking protocols. Current implementation accepts ZDOCK output files.
2. zdock-parser: Parses ZDOCK output files, generates and returns the coordinates of poses without first writing to PDB files.
3. docking-eval: Implements the CAPRI criteria to evaluate docking results with respect to a reference structure.
4. drsip-common: Common functions used by the other modules.

If you're using any of our packages please cite us

How to Install DR-SIP?

There are 2 ways to install the DR-SIP, using conda (recommended) or pip.

Conda Installation

We recommend that you install the Anaconda distribution for Python 2.7.

To install DR-SIP:

conda config --append channels conda-forge
conda config --append channels drsip
conda install drsip

Pip Installation

For pip:

pip install drsip

How to Use?

Membrane Protein Docking Protocol

drsip membrane static-pdb-file mobile-pdb-file trans-helix zdock-output-file -d distance-restraints-file -o DRSIP-results.csv -p top20/

The trans-helix argument is a string containing comma separated resids of each transmembrane helix. Example: "17-46, 69-93", where the first transmembrane helix is from resid 17 to 46 and the second is from resid 69 to 93. Transmembrane helix assignments can be obtained from the Orientations of Proteins in Membranes database.

While the -o argument is for writing the results of top 20 poses to an CSV file and -p is the folder to write out the PDB files of the top 20 complexes generated from the top 20 poses.

The distance restraints file is optional, the filter will not be applied if there are no distance restraints. Each line in the distance restraints file contains a residue pair formatted as:

chainID1 resID1 chainID2 resID2 distance

NOTE: The columns are separated by tabs (tab-delimited).

Soluble Protein Protocol

drsip soluble static-pdb-file mobile-pdb-file zdock-output-file distance-restraints-file -o DRSIP-results.csv -p top20/

Similar to running the membrane protein docking protocol except that the distance restraints file is required and there is no trans-helix argument.

Examples:

Download the examples here and extract the zip file.

First, change the current working directory to the examples folder:

cd examples

Then for the HoTP system, MscL:

drsip membrane 2oar_static_marked.pdb 2oar_mobile_marked.pdb "17-46, 69-93" MscL_54000_ZDOCK.out -d MscL_FRET_Data.txt -o MscL/DRSIP_results.csv -p MscL/

where "17-46, 69-93" are the 2 transmembrane helices assigned by OPM. The results table and top 20 complexes will be written into the MscL folder.

While, MscL_FRET_Data.txt contains:

A	40	B	40	5.033146272
B	25	A	25	4.528073406
...

For more details run "drsip membrane -h" or see the documentation.

As for the soluble system, Syt1-SNARE:

drsip soluble 5ccg_SNARE_marked.pdb 2r83_aligned_domains_marked.pdb Syt1-SNARE_ZDOCK_54000.out Syt1-SNARE_FRET_Data.txt -o Syt1_SNARE/DRSIP_results.csv -p Syt1_SNARE/

The results table and the top 20 poses will be written into the Syt1_SNARE folder.

For more details run "drsip soluble -h" or see the documentation.

See the MscL_ref and Syt1_SNARE_ref folders for the pre-computed results.

Documentation

Full documentation available here

How to Cite Us?

If you use any part of the DR-SIP package please cite us:

Chan Justin, Chien Chi-Hong Chang, Zou Jinhao, Pan Rong-Long, Yang Lee-Wei.
(2019) DR-SIP: Protocols for Higher Order Structure Modeling with Distance
Restraints- and Cyclic Symmetry-Imposed Packing. BioRxiv [Preprint].
Available at: https://doi.org/10.1101/500397.

Manuscript is available on the preprint site BioRxiv.

References

The DR-SIP package uses the following packages:

1. MDAnalysis
2. BioPython
3. NumPy
4. SciPy
5. Numba
6. Pandas
7. u-msgpack-python.