Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 71,071 bioRxiv papers from 310,049 authors.

Flexible backbone assembly and refinement of symmetrical homomeric complexes

By Shourya S. Roy Burman, Remy A. Yovanno, Jeffrey J. Gray

Posted 06 Sep 2018
bioRxiv DOI: 10.1101/409730 (published DOI: 10.1016/j.str.2019.03.014)

Symmetrical homomeric proteins are ubiquitous in every domain of life, and information about their structure is essential to decipher function. The size of these complexes often makes them intractable to high-resolution structure determination experiments. Computational docking algorithms offer a promising alternative for modeling large complexes with arbitrary symmetry. Accuracy of existing algorithms, however, is limited by backbone inaccuracies when using homology-modeled monomers. Here, we present Rosetta SymDock2 with a broad search of symmetrical conformational space using a six-dimensional coarse-grained score function followed by an all-atom flexible-backbone refinement, which we demonstrate to be essential for physically-realistic modeling of tightly packed complexes. In global docking of a benchmark set of complexes of different point symmetries -- staring from homology-modeled monomers -- we successfully dock (defined as predicting three near-native structures in the five top-scoring models) 19 out of 31 cyclic complexes and 5 out of 12 dihedral complexes.

Download data

  • Downloaded 446 times
  • Download rankings, all-time:
    • Site-wide: 26,214 out of 71,071
    • In biophysics: 998 out of 3,026
  • Year to date:
    • Site-wide: 27,223 out of 71,071
  • Since beginning of last month:
    • Site-wide: 11,652 out of 71,071

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News