Computational modeling of protein assemblies

Current Opinion in Structural Biology
Neelesh Soni, M S Madhusudhan

Abstract

Computational methods to predict the 3D structures of protein interactions fall into 3 categories-template based modeling, protein-protein docking and hybrid/integrative modeling. The two most important considerations for modeling methods are sampling and scoring conformations. Sampling has benefitted from techniques such as fast Fourier transforms (FFT), spherical harmonics and higher order manifolds. Scoring complexes to determine binding free energy is still a challenging problem. Rapid advances have been made in hybrid modeling where experimental data are amalgamated with computations. These methods have received a boost from the popularity of experimental methods such as electron microscopy (EM). While increasingly larger and complicated complexes are now getting elucidated by integrative methods, modeling conformational flexibility remains a challenge. Ongoing improvements to these techniques portend a future where organelles or even cells could be accurately modeled at a molecular level.

References

Oct 18, 2015·The Journal of Biological Chemistry·Jaclyn LoPiccoloJonathan M Backer

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Citations

Feb 22, 2018·Reviews in the Neurosciences·Diego GuidolinLuigi F Agnati
Jan 4, 2018·Proceedings of the National Academy of Sciences of the United States of America·Maxx H TessmerDara W Frank
Aug 6, 2019·Plant, Cell & Environment·Paula da Fonseca-PereiraDanilo M Daloso
Jan 18, 2020·Briefings in Bioinformatics·Ammu Prasanna KumarSuryani Lukman
Apr 5, 2020·Bioinformatics·Abhilesh S DhawanjewarMallur S Madhusudhan
Aug 15, 2019·Scientific Data·Xinyue KangHeng Zheng
May 25, 2021·Frontiers in Molecular Biosciences·Sundeep Chaitanya VedithiTom L Blundell
Jun 22, 2021·Frontiers in Molecular Biosciences·Alejandro Soto-OspinaAndrés Villegas Lanau
Aug 16, 2018·Journal of Chemical Theory and Computation·Hervé HoguesEnrico O Purisima

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