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Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server

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Protein-Protein Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2690))

Abstract

Interactions of proteins with other macromolecules have important structural and functional roles in the basic processes of living cells. To understand and elucidate the mechanisms of interactions, it is important to know the 3D structures of the complexes. Proteomes contain numerous protein-protein complexes, for which experimentally determined structures often do not exist. Computational techniques can be a practical alternative to obtain useful complex structure models. Here, we present a web server that provides access to the LZerD and Multi-LZerD protein docking tools, which can perform both pairwise and multi-chain docking. The web server is user-friendly, with options to visualize the distribution and structures of binding poses of top-scoring models. The LZerD web server is available at https://lzerd.kiharalab.org. This chapter dictates the algorithm and step-by-step procedure to model the monomeric structures with AttentiveDist, and also provides the detail of pairwise LZerD docking, and multi-LZerD. This also provided case studies for each of the three modules.

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Acknowledgments

This work was partly supported by the National Institutes of Health (R01GM133840, R01GM123055, and 3R01GM133840-02S1) and the National Science Foundation (CMMI1825941, MCB1925643, DBI2146026, and DBI2003635). HK and MMG are supported by the Science & Engineering Research Board (SERB), Government of India through the Overseas Visiting Doctoral Fellowship program (OVDF). MMG is partially supported by the Science and Engineering Research Board (SERB), Ministry of Science and Technology, Government of India (No. CRG/2020/000314). CC was supported by a NIGMS-funded predoctoral fellowship (T32 GM132024). The contents of the chapter are solely the responsibility of the authors and do not represent the official views of the NIGMS or NIH.

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Correspondence to Daisuke Kihara .

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Harini, K., Christoffer, C., Gromiha, M.M., Kihara, D. (2023). Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server. In: Mukhtar, S. (eds) Protein-Protein Interactions. Methods in Molecular Biology, vol 2690. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3327-4_28

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  • DOI: https://doi.org/10.1007/978-1-0716-3327-4_28

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  • Publisher Name: Humana, New York, NY

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  • Online ISBN: 978-1-0716-3327-4

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