Challenges in protein docking

•Docking developments aim at improvement of modeling macromolecular complexes.•Challenges include proper accounting for conformational flexibility.•Docking methods benefit from new data on protein interactions.•New developments focus on realistic modeling of protein interactions in vivo. Current dev...

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Bibliographic Details
Published in:Current opinion in structural biology 2020-10, Vol.64, p.160-165
Main Author: Vakser, Ilya A
Format: Article
Language:English
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Summary:•Docking developments aim at improvement of modeling macromolecular complexes.•Challenges include proper accounting for conformational flexibility.•Docking methods benefit from new data on protein interactions.•New developments focus on realistic modeling of protein interactions in vivo. Current developments in protein docking aim at improvement of applicability, accuracy and utility of modeling macromolecular complexes. The challenges include the need for greater emphasis on protein docking to molecules of different types, proper accounting for conformational flexibility upon binding, new promising methodologies based on residue co-evolution and deep learning, affinity prediction, and further development of fully automated docking servers. Importantly, new developments increasingly focus on realistic modeling of protein interactions in vivo, including crowded environment inside a cell, which involves multiple transient encounters, and propagating the system in time. This opinion paper offers the author's perspective on these challenges in structural modeling of protein interactions and the future of protein docking.
ISSN:0959-440X
1879-033X
DOI:10.1016/j.sbi.2020.07.001