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Path-LZerD: Multimeric Protein Complex Assembly Order Prediction
Updates
Introduction Path-LZerD predicts the assembly order of a protein complex by simulating its assembly process. Many important functions in a cell are carried out by protein complexes with more than two subunits. Similar to folding of a single protein, multimeric protein complexes in general follow an energetically-favored assembly path. Path-LZerD predicts the assembly path of a complex by simulating docking process of the complex. Path-LZerD takes subunit structures as input, assembles them into protein complex models using a multimeric protein docking protocol, and predicts assemble pathway of the complex from actually observed pathways in the docking process. Overview of Path-LZerD
Path-LZerD uses a multiple-protein docking algorithm (Multi-LZerD) which assembles a protein complex structure from individual subunit structures. By analyzing the assembly pathways of predicted complex models, Path-LZerD predicts the assembly order of the protein complex. Download Path-LZerD The current version of Path-LZerD as used in the paper is available as a zip file.Download Path-LZerD Programs. Download MultiLZerD for Path-LZerD. Download Case1 Data (1a0r) Download Case2 Data (1gpq) Download Case3 Data (1w88) Tutorial Getting Started
Download and save the zip file of the program in your preferred directory.
The files can be unpacked using the commands:
The generated Directory contains the files:
Path-LZerD requires a pairwise protein docking program LZerD and a multiple protein docking program Multi-LZerD. They are available in the LZerD docking suite at the Kihara Lab website: LZerd page and Multi-LZerD page. Path-LZerD also requires the following external programs and python modules:
Running the Program Path-LZerD to make assembly path prediction using the output files (.ga.out) of Multi-LZerD. Before running the Path-LZerD script, users have to put the following files to the same directory. Here, we explain how to run Path-LZerD on the sample data, which are provided in the test directory.
In the test directory, run_test.sh was described as
After preparing all files, the Path-LZerD protocol will be executed by Result
The predicted assembly order is recorded in finalgene_chain.csv:
These files show path prediction using the different scoring functions using the final generation method. The first column is showing the type of scoring function, except “sumrank”. The “sumrank” is the prediction made by using the sum of score rank by DFIRE, SOAPPP, GOAP, molecular mechanics (Molmec), LZerD shape score (shapescore), OPUSPSP, and ITScore. The second column is showing the predicted assembly order. For example, “BG>BGP” means chain B and G form a subcomplex first, then B-G complex bounds with chain P.
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