Fold prediction of helical proteins using torsion angle dynamics and predicted restraints

Proceedings of the National Academy of Sciences of the United States of America
Chao ZhangSung-Hou Kim

Abstract

We describe a procedure for predicting the tertiary folds of alpha-helical proteins from their primary sequences. The central component of the procedure is a method for predicting interhelical contacts that is based on a helix-packing model. Instead of predicting the individual contacts, our method attempts to identify the entire patch of contacts that involve residues regularly spaced in the sequences. We use this component to glue together two powerful existing methods: a secondary structure prediction program, whose output serves as the input to the contact prediction algorithm, and the tortion angle dynamics program, which uses the predicted tertiary contacts and secondary structural states to assemble three-dimensional structures. In the final step, the procedure uses the initial set of simulated structures to refine the predicted contacts for a new round of structure calculation. When tested against 24 small to medium-sized proteins representing a wide range of helical folds, the completely automated procedure is able to generate native-like models within a limited number of trials consistently.

References

Mar 1, 1979·International Journal of Peptide and Protein Research·G M Crippen
May 1, 1995·Protein Science : a Publication of the Protein Society·C Mumenthaler, W Braun
Mar 1, 1994·Protein Engineering·W R Taylor, K Hatrick
May 10, 1994·Proceedings of the National Academy of Sciences of the United States of America·J U Bowie, D Eisenberg
Apr 1, 1994·Proteins·U GöbelA Valencia
Apr 1, 1996·Current Opinion in Structural Biology·R L Jernigan, I Bahar
Nov 1, 1996·Protein Engineering·D J ThomasC Sander
Mar 1, 1997·Protein Science : a Publication of the Protein Society·J SkolnickA Godzik
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Nov 14, 1997·Nature Structural Biology·J U Bowie
Nov 21, 1997·Journal of Molecular Biology·P GüntertK Wüthrich
Jan 1, 1997·Journal of Magnetic Resonance·E G SteinA T Brünger
Oct 30, 1998·Quarterly Reviews of Biophysics·P Güntert
Mar 8, 2000·Proceedings of the National Academy of Sciences of the United States of America·C Zhang, S H Kim
Jun 14, 2000·Current Opinion in Structural Biology·S H Kim

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Citations

Jun 16, 2006·Journal of Computer-aided Molecular Design·Roman G EfremovAlexander S Arseniev
Jan 27, 2005·Bioinformatics·Andreas MöglichHans Robert Kalbitzer
Nov 10, 2005·Journal of Bioinformatics and Computational Biology·Hongzhi Li, Yaoqi Zhou
Apr 2, 2004·Proceedings of the National Academy of Sciences of the United States of America·Steve S HuangP Leslie Dutton
Feb 7, 2003·Proceedings of the National Academy of Sciences of the United States of America·Marian NaniasHarold A Scheraga
Aug 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Sung-Hou KimKyeong Kyu Kim
May 15, 2007·Biophysical Journal·Hongyi Zhou, Jeffrey Skolnick
Aug 29, 2014·PloS One·Harinder SinghGajendra P S Raghava
Mar 19, 2005·Chembiochem : a European Journal of Chemical Biology·Yan ZhangPhilip S Portoghese
Jul 11, 2006·Magnetic Resonance in Chemistry : MRC·Stephen NealDavid S Wishart
Sep 28, 2005·Proteins·Osvaldo GrañaAlfonso Valencia
Aug 8, 2015·Physical Review Letters·Matthew J Williams, Michael Bachmann
Jul 15, 2016·Physical Review. E·Matthew J Williams, Michael Bachmann
Jun 27, 2016·Polymers·Matthew J Williams, Michael Bachmann
Jul 18, 2017·The Journal of Chemical Physics·Matthew J Williams, Michael Bachmann

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