Feature space resampling for protein conformational search.

Proteins
Ben BlumDavid Baker

Abstract

De novo protein structure prediction requires location of the lowest energy state of the polypeptide chain among a vast set of possible conformations. Powerful approaches include conformational space annealing, in which search progressively focuses on the most promising regions of conformational space, and genetic algorithms, in which features of the best conformations thus far identified are recombined. We describe a new approach that combines the strengths of these two approaches. Protein conformations are projected onto a discrete feature space which includes backbone torsion angles, secondary structure, and beta pairings. For each of these there is one "native" value: the one found in the native structure. We begin with a large number of conformations generated in independent Monte Carlo structure prediction trajectories from Rosetta. Native values for each feature are predicted from the frequencies of feature value occurrences and the energy distribution in conformations containing them. A second round of structure prediction trajectories are then guided by the predicted native feature distributions. We show that native features can be predicted at much higher than background rates, and that using the predicted feature dis...Continue Reading

References

May 30, 1998·Journal of Molecular Biology·K W PlaxcoD Baker
Feb 3, 1999·Bioinformatics·K KarplusR Hughey
Apr 6, 2001·Physical Review Letters·F Wang, D P Landau
Oct 7, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jens Meiler, David Baker
Oct 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Bin QianDavid Baker
Jun 18, 2005·Bioinformatics·T J Brunette, Oliver Brock
Apr 16, 2008·Annual Review of Biochemistry·Rhiju Das, David Baker
Aug 4, 2009·Journal of Molecular Biology·David E KimDavid Baker

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Citations

Jan 24, 2013·Proceedings of the National Academy of Sciences of the United States of America·Nicholette Zeliadt
Jul 26, 2012·PloS One·David SimonciniKam Y J Zhang
Jan 19, 2016·Journal of Molecular Biology·Kala Bharath PillaThomas Huber
May 24, 2011·Current Opinion in Structural Biology·Robert J PantazesCostas D Maranas
Apr 23, 2014·Proteins·Rojan Shrestha, Kam Y J Zhang
May 10, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gideon K GogoviEstela Blaisten-Barojas

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