Proteins interact with each other and organize themselves into macromolecular machines (ie. complexes) to carry out essential functions of the cell. We have a good understanding of a few complexes such as the proteasome and the ribosome but currently we have an incomplete view of all protein complexes as well as their functions. The yeast.MAP attempts to address this lack of understanding by integrating several large scale protein interaction datasets to obtain a comprehensive view of protein complexes. In yeast.MAP we integrated large scale affinity enrichment mass spectrometry (AP/MS) datasets from Michaelis et al., probabilistic scoring of large-scale mass spectrometry data sets (Hart et al.), and deep-learning based PPI prediction (Humphreys et al.) to produce a yeast complex map with ~800 complexes.

Contributers

  Kevin Drew (website)

Funding

  NIH R00, NSF/BBSRC

Citation

• Coming soon.

References

• André C. Michaelis, Andreas-David Brunner, Maximilian Zwiebel, Florian Meier, Maximilian T. Strauss, Isabell Bludau & Matthias Mann The social and structural architecture of the yeast protein interactome Nature volume 624, pages 192–200 (2023)
• Ian R. Humphreys, Jimin Pei, Minkyung Baek, Aditya Krishnakumar, Ivan Anishchenko, Sergey Ovchinnikov, Jing Zhang, Travis J. Ness, Sudeep Banjade, Saket R. Bagde, Viktoriya G. Stancheva, Xiao-Han Li, Kaixian Liu, Zhi Zheng, Daniel J. Barrero, Upasana Roy, Jochen Kuper, Israel S. Fernández, Barnabas Szakal, Dana Branzei, Josep Rizo, Caroline Kisker, Eric C. Greene, Sue Biggins, Scott Keeney, Elizabeth A. Miller, J. Christopher Fromme, Tamara L. Hendrickson, Qian Cong, David Baker Computed structures of core eukaryotic protein complexes Science 11 Nov 2021 Vol 374, Issue 6573 DOI: 10.1126/science.abm4805
• G Traver Hart, Insuk Lee & Edward M Marcotte A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality BMC Bioinformatics 8, 236 (2007). https://doi.org/10.1186/1471-2105-8-236

Contact

  proteincomplexmap (at) gmail.com