Abstract
Protein-protein docking is a useful tool for modeling the structures of protein complexes that have yet to be experimentally determined. Understanding the structures of protein complexes is a key component for formulating hypotheses in biophysics regarding the functional mechanisms of complexes. Protein-protein docking is an established technique for cases where the structures of the subunits have been determined. While the number of known structures deposited in the Protein Data Bank is increasing, there are still many cases where the structures of individual proteins that users want to dock are not determined yet. Here, we have integrated the AttentiveDist method for protein structure prediction into our LZerD webserver for protein-protein docking, which enables users to simply submit protein sequences and obtain full-complex atomic models, without having to supply any structure themselves. We have further extended the LZerD docking interface with a symmetrical homodimer mode. The LZerD server is available at https://lzerd.kiharalab.org/.
Highlights
Protein-protein interactions are key components of many biological processes, and the threedimensional (3D) structures of the protein-protein complexes formed are a crucial resource for reasoning about their molecular functions
We present the current version of the LZerD webserver, with new functionality of de novo prediction of subunit structures by AttentiveDist and applying symmetry constraints for homodimer modeling
As the LZerD server group did during CAPRI, here we used an unbound structure from X-ray crystallography provided by the organizers for IL23, which has a root-mean-square deviation (RMSD) of 1.7 Å to the native T122 structure
Summary
Protein-protein interactions are key components of many biological processes, and the threedimensional (3D) structures of the protein-protein complexes formed are a crucial resource for reasoning about their molecular functions. Structures of these complexes would be determined experimentally, through techniques such as X-ray crystallography or cryo-electron microscopy. It is possible to instead use computational methods to construct atomic structure models of protein complexes (Aderinwale et al, 2020) This class of methods is called protein-protein docking, and suitably constructed models from docking can be used to reason about how molecular functions are carried out in the living cell, even in the absence of an experimentally determined complex structure (Sanyal et al, 2021). The LZerD suite of methods has been ranked at or near the top of all server groups in recent rounds of CAPRI (Lensink et al, 2018; Lensink et al, 2019; Lensink et al, 2020), the blind communitywide assessment of protein docking methods
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