LZerD is an algorithm for predicting the structure of protein complexes based on receptor and ligand subunit structures, also known as protein-protein docking. Multi-LZerD is an extension of LZerD that can dock three or more protein subunit structures simultaneously.
What is LZerD useful for?
LZerD is useful wherever biological questions can be answered by a structure or by an ensemble of structures. In general, structure models can elucidate how two proteins interact physically and can indicate interface residues. We have used LZerD in collaboration with experimentalists on many different topics, including for example:
regulation of enzyme activity
regulation of histone modification
regulation of unfolded protein response
How will I get results?
When your job finishes, you will receive an email with a link to the results page. The results page shows a summary visualization of the distribution of docking models, and has options for viewing and downloading the models.
How can I view the models LZerD generates?
The results page for completed LZerD jobs features a visualizer you can use to view the distribution of ligand positions as well as individual models. To generate more complex visualizations or to generate publication-quality figures, we recommend using standalone visualization software such as PyMOL. Models can be downloaded from the results page either individually or in bulk.
How accurate will the results be?
Typically, protein-protein docking works best when the input subunit structures are accurately modeled. In the CAPRI community-wide complex structure prediction experiment, our team performs competitively among the top groups (see References).
I'm not sure how to best apply LZerD to my problem. Can you help me?
Of course! We are always looking for new collaborations. Please contact us.
Can I use a different scoring function to rank the output models?
You can apply any custom scoring function by downloading the whole output model set and running your scoring function locally.
How long does LZerD take to run?
Depending on the size of the input subunits, parameter choices, and availability of cluster resources, the LZerD server generally take a few minutes to a few hours to return results. For example, using a surface reduction cutoff of 1e-2 will yield results sooner, but the default of 1e-4 searches more conformations.
Can I download LZerD/Multi-LZerD and run it locally?
Yes. LZerD is made available here, and Multi-LZerD is made available here.
Can I submit large numbers of jobs to the LZerD server?
If you want to submit large numbers of jobs, you should contact us.
Should I use the LZerD server to dock peptides or intrinsically disordered proteins?
No. You should instead use our method IDP-LZerD, which has been designed to handle disordered proteins. The code of IDP-LZerD is made available here.
Should I use the LZerD server to dock more than two subunits at once?
Yes. By clicking the Multi-LZerD button on the job submission page, you can use our multiple docking method Multi-LZerD, which has been designed to dock more than two subunits simultaneously. Multi-LZerD is also made available for download in standalone form here.
Should I use the LZerD server to dock small molecules such as drug molecules?
No. The ranksum scoring method currently is only designed to handle proteins. Given an individual small molecule conformer, LZerD can generate models based on shape complementarity alone.
Should I use the LZerD server to dock nucleic acids?
No. The ranksum scoring method currently is only designed to handle proteins. Given a nucleic acid structure, LZerD can generate models based on shape complementarity alone.
Can I use LZerD for commercial purposes?
The LZerD server should only be used for noncommercial purposes. If you want to use LZerD for commercial purposes, you should contact us.
Is there a video tutorial available?
This video tutorial describes the docking method and demonstrates how to use the server: