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Items: 50

1.

A modelling paradigm for RNA virus assembly.

Twarock R, Bingham RJ, Dykeman EC, Stockley PG.

Curr Opin Virol. 2018 Aug 2. pii: S1879-6257(18)30006-3. doi: 10.1016/j.coviro.2018.07.003. [Epub ahead of print] Review.

2.

Hamiltonian path analysis of viral genomes.

Twarock R, Leonov G, Stockley PG.

Nat Commun. 2018 May 22;9(1):2021. doi: 10.1038/s41467-018-03713-y. No abstract available.

3.

RNA Virus Evolution via a Quasispecies-Based Model Reveals a Drug Target with a High Barrier to Resistance.

Bingham RJ, Dykeman EC, Twarock R.

Viruses. 2017 Nov 17;9(11). pii: E347. doi: 10.3390/v9110347.

4.

Rewriting nature's assembly manual for a ssRNA virus.

Patel N, Wroblewski E, Leonov G, Phillips SEV, Tuma R, Twarock R, Stockley PG.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12255-12260. doi: 10.1073/pnas.1706951114. Epub 2017 Oct 30.

5.

A30 Recombination & evolution in two viral families: effective steps or a random walk?

Bingham R, Leonov G, Patel N, Weiss E, White S, Dykeman E, Stockley P, Twarock R.

Virus Evol. 2017 Mar 5;3(Suppl 1). pii: vew036.029. doi: 10.1093/ve/vew036.029. eCollection 2017 Mar. No abstract available.

6.

Erratum: Genomic RNA folding mediates assembly of human parechovirus.

Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJB, Butcher SJ, Stockley PG, Twarock R.

Nat Commun. 2017 Jul 14;8(1):83. doi: 10.1038/s41467-017-00026-4.

7.

A proposed simulation method for directed self-assembly of nanographene.

Geraets JA, Baldwin JPC, Twarock R, Hancock Y.

J Phys Condens Matter. 2017 Sep 6;29(35):355901. doi: 10.1088/1361-648X/aa7c0b. Epub 2017 Jun 27.

8.

HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly.

Patel N, White SJ, Thompson RF, Bingham R, Weiß EU, Maskell DP, Zlotnick A, Dykeman E, Tuma R, Twarock R, Ranson NA, Stockley PG.

Nat Microbiol. 2017 Jun 19;2:17098. doi: 10.1038/nmicrobiol.2017.98.

9.

Impact of Hydrogen Bonding in the Binding Site between Capsid Protein and MS2 Bacteriophage ssRNA.

Poudel L, Twarock R, Steinmetz NF, Podgornik R, Ching WY.

J Phys Chem B. 2017 Jul 6;121(26):6321-6330. doi: 10.1021/acs.jpcb.7b02569. Epub 2017 Jun 21.

PMID:
28581757
10.

Classification of self-assembling protein nanoparticle architectures for applications in vaccine design.

Indelicato G, Burkhard P, Twarock R.

R Soc Open Sci. 2017 Apr 26;4(4):161092. doi: 10.1098/rsos.161092. eCollection 2017 Apr.

11.

Genomic RNA folding mediates assembly of human parechovirus.

Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJB, Butcher SJ, Stockley PG, Twarock R.

Nat Commun. 2017 Feb 23;8(1):5. doi: 10.1038/s41467-016-0011-z. Erratum in: Nat Commun. 2017 Jul 14;8(1):83.

12.

Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid.

Stockley PG, White SJ, Dykeman E, Manfield I, Rolfsson O, Patel N, Bingham R, Barker A, Wroblewski E, Chandler-Bostock R, Weiß EU, Ranson NA, Tuma R, Twarock R.

Bacteriophage. 2016 Mar 2;6(1):e1157666. eCollection 2016 Jan-Mar.

13.

Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging.

Stewart H, Bingham RJ, White SJ, Dykeman EC, Zothner C, Tuplin AK, Stockley PG, Twarock R, Harris M.

Sci Rep. 2016 Mar 14;6:22952. doi: 10.1038/srep22952.

14.

Principles Governing the Self-Assembly of Coiled-Coil Protein Nanoparticles.

Indelicato G, Wahome N, Ringler P, Müller SA, Nieh MP, Burkhard P, Twarock R.

Biophys J. 2016 Feb 2;110(3):646-660. doi: 10.1016/j.bpj.2015.10.057.

15.

Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2.

Rolfsson Ó, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG.

J Mol Biol. 2016 Jan 29;428(2 Pt B):431-48. doi: 10.1016/j.jmb.2015.11.014. Epub 2015 Dec 1.

16.

Orbits of crystallographic embedding of non-crystallographic groups and applications to virology.

Twarock R, Valiunas M, Zappa E.

Acta Crystallogr A Found Adv. 2015 Nov;71(Pt 6):569-82. doi: 10.1107/S2053273315015326. Epub 2015 Sep 22.

PMID:
26522406
17.

Approximation of virus structure by icosahedral tilings.

Salthouse DG, Indelicato G, Cermelli P, Keef T, Twarock R.

Acta Crystallogr A Found Adv. 2015 Jul;71(Pt 4):410-22. doi: 10.1107/S2053273315006701. Epub 2015 May 29.

PMID:
26131897
18.

Asymmetric genome organization in an RNA virus revealed via graph-theoretical analysis of tomographic data.

Geraets JA, Dykeman EC, Stockley PG, Ranson NA, Twarock R.

PLoS Comput Biol. 2015 Mar 20;11(3):e1004146. doi: 10.1371/journal.pcbi.1004146. eCollection 2015 Mar.

19.

Revealing the density of encoded functions in a viral RNA.

Patel N, Dykeman EC, Coutts RH, Lomonossoff GP, Rowlands DJ, Phillips SE, Ranson N, Twarock R, Tuma R, Stockley PG.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2227-32. doi: 10.1073/pnas.1420812112. Epub 2015 Feb 2.

20.

On the subgroup structure of the hyperoctahedral group in six dimensions.

Zappa E, Dykeman EC, Twarock R.

Acta Crystallogr A Found Adv. 2014 Sep;70(Pt 5):417-28. doi: 10.1107/S2053273314007712. Epub 2014 Jul 10.

21.

Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy.

Dykeman EC, Stockley PG, Twarock R.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5361-6. doi: 10.1073/pnas.1319479111. Epub 2014 Mar 24.

22.

Viruses and fullerenes--symmetry as a common thread?

Dechant PP, Wardman J, Keef T, Twarock R.

Acta Crystallogr A Found Adv. 2014 Mar;70(Pt 2):162-7. doi: 10.1107/S2053273313034220. Epub 2014 Feb 18.

PMID:
24572317
23.

Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition.

Polles G, Indelicato G, Potestio R, Cermelli P, Twarock R, Micheletti C.

PLoS Comput Biol. 2013;9(11):e1003331. doi: 10.1371/journal.pcbi.1003331. Epub 2013 Nov 14.

24.

Nonicosahedral pathways for capsid expansion.

Cermelli P, Indelicato G, Twarock R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Sep;88(3):032710. Epub 2013 Sep 16.

25.

Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome.

Dykeman EC, Stockley PG, Twarock R.

J Mol Biol. 2013 Sep 9;425(17):3235-49. doi: 10.1016/j.jmb.2013.06.005. Epub 2013 Jun 11.

PMID:
23763992
26.

Packaging signals in single-stranded RNA viruses: nature's alternative to a purely electrostatic assembly mechanism.

Stockley PG, Twarock R, Bakker SE, Barker AM, Borodavka A, Dykeman E, Ford RJ, Pearson AR, Phillips SE, Ranson NA, Tuma R.

J Biol Phys. 2013 Mar;39(2):277-87. doi: 10.1007/s10867-013-9313-0. Epub 2013 Apr 12.

27.

Building a viral capsid in the presence of genomic RNA.

Dykeman EC, Stockley PG, Twarock R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Feb;87(2):022717. Epub 2013 Feb 25.

PMID:
23496558
28.

Structural constraints on the three-dimensional geometry of simple viruses: case studies of a new predictive tool.

Keef T, Wardman JP, Ranson NA, Stockley PG, Twarock R.

Acta Crystallogr A. 2013 Mar;69(Pt 2):140-50. doi: 10.1107/S0108767312047150. Epub 2013 Jan 8.

29.

On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: a Brownian dynamics study.

ElSawy KM, Verma CS, Joseph TL, Lane DP, Twarock R, Caves LS.

Cell Cycle. 2013 Feb 1;12(3):394-404. doi: 10.4161/cc.23511. Epub 2013 Jan 16.

30.

Peptide inhibitors of viral assembly: a novel route to broad-spectrum antivirals.

ElSawy KM, Twarock R, Verma CS, Caves LS.

J Chem Inf Model. 2012 Mar 26;52(3):770-6. doi: 10.1021/ci200467s. Epub 2012 Mar 6.

PMID:
22390317
31.

Characterization of the Ligand Receptor Encounter Complex and Its Potential for in Silico Kinetics-Based Drug Development.

ElSawy KM, Twarock R, Lane DP, Verma CS, Caves LS.

J Chem Theory Comput. 2012 Jan 10;8(1):314-21. doi: 10.1021/ct200560w. Epub 2011 Dec 28.

PMID:
26592892
32.

On the origin of order in the genome organization of ssRNA viruses.

ElSawy KM, Caves LS, Twarock R.

Biophys J. 2011 Aug 17;101(4):774-80. doi: 10.1016/j.bpj.2011.07.005.

33.

Degenerate RNA packaging signals in the genome of Satellite Tobacco Necrosis Virus: implications for the assembly of a T=1 capsid.

Bunka DH, Lane SW, Lane CL, Dykeman EC, Ford RJ, Barker AM, Twarock R, Phillips SE, Stockley PG.

J Mol Biol. 2011 Oct 14;413(1):51-65. doi: 10.1016/j.jmb.2011.07.063. Epub 2011 Aug 3.

PMID:
21839093
34.

A crystallographic approach to structural transitions in icosahedral viruses.

Indelicato G, Cermelli P, Salthouse DG, Racca S, Zanzotto G, Twarock R.

J Math Biol. 2012 Apr;64(5):745-73. doi: 10.1007/s00285-011-0425-5. Epub 2011 May 25.

PMID:
21611828
35.

Simple rules for efficient assembly predict the layout of a packaged viral RNA.

Dykeman EC, Grayson NE, Toropova K, Ranson NA, Stockley PG, Twarock R.

J Mol Biol. 2011 May 6;408(3):399-407. doi: 10.1016/j.jmb.2011.02.039. Epub 2011 Feb 25. Review.

PMID:
21354423
36.

The physics of virus assembly. Preface.

Stockley PG, Twarock R.

Phys Biol. 2010 Dec 9;7(4):040301. doi: 10.1088/1478-3975/7/4/040301. No abstract available.

PMID:
21149977
37.

The impact of viral RNA on assembly pathway selection.

Morton VL, Dykeman EC, Stonehouse NJ, Ashcroft AE, Twarock R, Stockley PG.

J Mol Biol. 2010 Aug 13;401(2):298-308. doi: 10.1016/j.jmb.2010.05.059. Epub 2010 Jun 1.

PMID:
20621589
38.

The impact of viral RNA on the association rates of capsid protein assembly: bacteriophage MS2 as a case study.

Elsawy KM, Caves LS, Twarock R.

J Mol Biol. 2010 Jul 23;400(4):935-47. doi: 10.1016/j.jmb.2010.05.037. Epub 2010 May 24.

PMID:
20562027
39.

All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein.

Dykeman EC, Twarock R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Mar;81(3 Pt 1):031908. Epub 2010 Mar 10.

PMID:
20365771
40.

Dynamic allostery controls coat protein conformer switching during MS2 phage assembly.

Dykeman EC, Stockley PG, Twarock R.

J Mol Biol. 2010 Feb 5;395(5):916-23. doi: 10.1016/j.jmb.2009.11.016. Epub 2009 Nov 12.

PMID:
19913554
41.

Affine extensions of the icosahedral group with applications to the three-dimensional organisation of simple viruses.

Keef T, Twarock R.

J Math Biol. 2009 Sep;59(3):287-313. doi: 10.1007/s00285-008-0228-5. Epub 2008 Nov 1.

PMID:
18979101
42.

Blueprints for viral capsids in the family of polyomaviridae.

Keef T, Twarock R, Elsawy KM.

J Theor Biol. 2008 Aug 21;253(4):808-16. doi: 10.1016/j.jtbi.2008.04.029. Epub 2008 May 4.

PMID:
18538795
43.

Dynamical implications of Viral Tiling Theory.

ElSawy KM, Taormina A, Twarock R, Vaughan L.

J Theor Biol. 2008 May 21;252(2):357-69. doi: 10.1016/j.jtbi.2008.02.003. Epub 2008 Feb 13.

PMID:
18353372
44.

The three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly.

Toropova K, Basnak G, Twarock R, Stockley PG, Ranson NA.

J Mol Biol. 2008 Jan 18;375(3):824-36. Epub 2007 Sep 7.

PMID:
18048058
45.

Mathematical virology: a novel approach to the structure and assembly of viruses.

Twarock R.

Philos Trans A Math Phys Eng Sci. 2006 Dec 15;364(1849):3357-73. Review.

46.

Master equation approach to the assembly of viral capsids.

Keef T, Micheletti C, Twarock R.

J Theor Biol. 2006 Oct 7;242(3):713-21. Epub 2006 May 16.

PMID:
16782135
47.

Crosslinking in viral capsids via tiling theory.

Twarock R, Hendrix RW.

J Theor Biol. 2006 Jun 7;240(3):419-24. Epub 2005 Dec 9.

PMID:
16337970
48.

Assembly models for Papovaviridae based on tiling theory.

Keef T, Taormina A, Twarock R.

Phys Biol. 2005 Sep 13;2(3):175-88.

PMID:
16224123
49.

Mathematical models for tubular structures in the family of Papovaviridae.

Twarock R.

Bull Math Biol. 2005 Sep;67(5):973-87. Epub 2004 Dec 21.

PMID:
15998491
50.

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