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Items: 1 to 50 of 64

1.

Frontiers in CryoEM Modeling.

Palermo G, Sugita Y, Wriggers W, Amaro RE.

J Chem Inf Model. 2019 Jul 22;59(7):3091-3093. doi: 10.1021/acs.jcim.9b00412. Epub 2019 Jun 13. No abstract available.

2.

Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics.

Kovacs JA, Galkin VE, Wriggers W.

BMC Struct Biol. 2018 Sep 15;18(1):12. doi: 10.1186/s12900-018-0089-0.

3.

Tracing Actin Filament Bundles in Three-Dimensional Electron Tomography Density Maps of Hair Cell Stereocilia.

Sazzed S, Song J, Kovacs JA, Wriggers W, Auer M, He J.

Molecules. 2018 Apr 11;23(4). pii: E882. doi: 10.3390/molecules23040882.

4.

A Balanced Approach to Adaptive Probability Density Estimation.

Kovacs JA, Helmick C, Wriggers W.

Front Mol Biosci. 2017 Apr 25;4:25. doi: 10.3389/fmolb.2017.00025. eCollection 2017.

5.

Computing Spatiotemporal Heat Maps of Lipid Electropore Formation: A Statistical Approach.

Wriggers W, Castellani F, Kovacs JA, Vernier PT.

Front Mol Biosci. 2017 Apr 25;4:22. doi: 10.3389/fmolb.2017.00022. eCollection 2017.

6.

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.

Zeil S, Kovacs J, Wriggers W, He J.

J Comput Biol. 2017 Jan;24(1):52-67. doi: 10.1089/cmb.2016.0145. Epub 2016 Dec 12.

7.

Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix.

He J, Zeil S, Hallak H, McKaig K, Kovacs J, Wriggers W.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2015 Nov;2015:1253-1259.

8.

Spatial Heat Maps from Fast Information Matching of Fast and Slow Degrees of Freedom: Application to Molecular Dynamics Simulations.

Kovacs JA, Wriggers W.

J Phys Chem B. 2016 Aug 25;120(33):8473-84. doi: 10.1021/acs.jpcb.6b02136. Epub 2016 May 31.

9.

Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis.

Alamo L, Qi D, Wriggers W, Pinto A, Zhu J, Bilbao A, Gillilan RE, Hu S, Padrón R.

J Mol Biol. 2016 Mar 27;428(6):1142-1164. doi: 10.1016/j.jmb.2016.01.027. Epub 2016 Feb 2.

10.

Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor.

Wahle M, Wriggers W.

PLoS Comput Biol. 2015 Oct 27;11(10):e1004516. doi: 10.1371/journal.pcbi.1004516. eCollection 2015 Oct.

11.

Numerical geometry of map and model assessment.

Wriggers W, He J.

J Struct Biol. 2015 Nov;192(2):255-61. doi: 10.1016/j.jsb.2015.09.011. Epub 2015 Sep 28.

12.

Developing a denoising filter for electron microscopy and tomography data in the cloud.

Starosolski Z, Szczepanski M, Wahle M, Rusu M, Wriggers W.

Biophys Rev. 2012 Sep 1;4(3):223-229.

13.
14.

An assembly model of rift valley Fever virus.

Rusu M, Bonneau R, Holbrook MR, Watowich SJ, Birmanns S, Wriggers W, Freiberg AN.

Front Microbiol. 2012 Jul 19;3:254. doi: 10.3389/fmicb.2012.00254. eCollection 2012.

15.

Conventions and workflows for using Situs.

Wriggers W.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):344-51. doi: 10.1107/S0907444911049791. Epub 2012 Mar 16.

16.

Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs.

Rusu M, Starosolski Z, Wahle M, Rigort A, Wriggers W.

J Struct Biol. 2012 May;178(2):121-8. doi: 10.1016/j.jsb.2012.03.001. Epub 2012 Mar 13.

17.

Outcome of the first electron microscopy validation task force meeting.

Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL.

Structure. 2012 Feb 8;20(2):205-14. doi: 10.1016/j.str.2011.12.014.

18.

Evolutionary bidirectional expansion for the tracing of alpha helices in cryo-electron microscopy reconstructions.

Rusu M, Wriggers W.

J Struct Biol. 2012 Feb;177(2):410-9. doi: 10.1016/j.jsb.2011.11.029. Epub 2011 Dec 6.

19.

Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization.

Zhang Z, Wriggers W.

Biochemistry. 2011 Mar 29;50(12):2144-56. doi: 10.1021/bi101843s. Epub 2011 Feb 18.

20.

Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes.

Birmanns S, Rusu M, Wriggers W.

J Struct Biol. 2011 Mar;173(3):428-35. doi: 10.1016/j.jsb.2010.11.002. Epub 2010 Nov 13.

21.

Atomic-level characterization of the structural dynamics of proteins.

Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W.

Science. 2010 Oct 15;330(6002):341-6. doi: 10.1126/science.1187409.

22.

Matching structural densities from different biophysical origins with gain and bias.

Wriggers W, Alamo L, Padrón R.

J Struct Biol. 2011 Mar;173(3):445-50. doi: 10.1016/j.jsb.2010.09.012. Epub 2010 Sep 18.

23.

Using Situs for the integration of multi-resolution structures.

Wriggers W.

Biophys Rev. 2010 Feb;2(1):21-27. Epub 2010 Jan 8.

24.

Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations.

Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE.

J Chem Theory Comput. 2009 Oct 13;5(10):2595-605. doi: 10.1021/ct900229u.

PMID:
26631775
25.

Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion.

Stember JN, Wriggers W.

J Chem Phys. 2009 Aug 21;131(7):074112. doi: 10.1063/1.3167410.

26.

Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity.

Alamo L, Wriggers W, Pinto A, Bártoli F, Salazar L, Zhao FQ, Craig R, Padrón R.

J Mol Biol. 2008 Dec 26;384(4):780-97. doi: 10.1016/j.jmb.2008.10.013. Epub 2008 Oct 14.

27.

Coarse-graining protein structures with local multivariate features from molecular dynamics.

Zhang Z, Wriggers W.

J Phys Chem B. 2008 Nov 6;112(44):14026-35. doi: 10.1021/jp806291p. Epub 2008 Oct 15.

28.

Biomolecular pleiomorphism probed by spatial interpolation of coarse models.

Rusu M, Birmanns S, Wriggers W.

Bioinformatics. 2008 Nov 1;24(21):2460-6. doi: 10.1093/bioinformatics/btn461. Epub 2008 Aug 30.

29.

Limulus polyphemus hemocyanin: 10 A cryo-EM structure, sequence analysis, molecular modelling and rigid-body fitting reveal the interfaces between the eight hexamers.

Martin AG, Depoix F, Stohr M, Meissner U, Hagner-Holler S, Hammouti K, Burmester T, Heyd J, Wriggers W, Markl J.

J Mol Biol. 2007 Mar 2;366(4):1332-50. Epub 2006 Dec 1.

PMID:
17207812
30.

Entropic folding pathway of human epidermal growth factor explored by disulfide scrambling and amplified collective motion simulations.

Zhang Z, Boyle PC, Lu BY, Chang JY, Wriggers W.

Biochemistry. 2006 Dec 26;45(51):15269-78. Epub 2006 Nov 30.

PMID:
17176049
31.

Multi-resolution anchor-point registration of biomolecular assemblies and their components.

Birmanns S, Wriggers W.

J Struct Biol. 2007 Jan;157(1):271-80. Epub 2006 Aug 25.

PMID:
17029847
32.
33.

Fast rotational matching of single-particle images.

Cong Y, Jiang W, Birmanns S, Zhou ZH, Chiu W, Wriggers W.

J Struct Biol. 2005 Nov;152(2):104-12. Epub 2005 Sep 30.

PMID:
16236526
34.

Control of protein functional dynamics by peptide linkers.

Wriggers W, Chakravarty S, Jennings PA.

Biopolymers. 2005;80(6):736-46. Review.

PMID:
15880774
35.

Direct observation of counterion organization in F-actin polyelectrolyte bundles.

Angelini TE, Liang H, Wriggers W, Wong GC.

Eur Phys J E Soft Matter. 2005 Apr;16(4):389-400.

PMID:
19177656
36.

Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering.

Arai R, Wriggers W, Nishikawa Y, Nagamune T, Fujisawa T.

Proteins. 2004 Dec 1;57(4):829-38.

PMID:
15390267
37.

Spanning the length scales of biomolecular simulation.

Wriggers W.

Structure. 2004 Jan;12(1):1-2. No abstract available.

38.

Interactive fitting augmented by force-feedback and virtual reality.

Birmanns S, Wriggers W.

J Struct Biol. 2003 Oct-Nov;144(1-2):123-31.

PMID:
14643215
39.

2D fast rotational matching for image processing of biophysical data.

Cong Y, Kovacs JA, Wriggers W.

J Struct Biol. 2003 Oct-Nov;144(1-2):51-60.

PMID:
14643208
40.

Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.

Opalka N, Chlenov M, Chacon P, Rice WJ, Wriggers W, Darst SA.

Cell. 2003 Aug 8;114(3):335-45.

41.

Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom.

Kovacs JA, Chacón P, Cong Y, Metwally E, Wriggers W.

Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1371-6. Epub 2003 Jul 23.

PMID:
12876338
42.

Like-charge attraction between polyelectrolytes induced by counterion charge density waves.

Angelini TE, Liang H, Wriggers W, Wong GC.

Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8634-7. Epub 2003 Jul 9.

43.

Mega-Dalton biomolecular motion captured from electron microscopy reconstructions.

Chacón P, Tama F, Wriggers W.

J Mol Biol. 2003 Feb 14;326(2):485-92.

PMID:
12559916
44.
45.

Fast rotational matching.

Kovacs JA, Wriggers W.

Acta Crystallogr D Biol Crystallogr. 2002 Aug;58(Pt 8):1282-6. Epub 2002 Jul 20.

PMID:
12136139
46.

Regulation of yeast actin behavior by interaction of charged residues across the interdomain cleft.

Yao X, Nguyen V, Wriggers W, Rubenstein PA.

J Biol Chem. 2002 Jun 21;277(25):22875-82. Epub 2002 Apr 8.

47.

Multi-resolution contour-based fitting of macromolecular structures.

Chacón P, Wriggers W.

J Mol Biol. 2002 Mar 29;317(3):375-84.

PMID:
11922671
48.

Conformational flexibility of bacterial RNA polymerase.

Darst SA, Opalka N, Chacon P, Polyakov A, Richter C, Zhang G, Wriggers W.

Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4296-301. Epub 2002 Mar 19.

49.

Modeling tricks and fitting techniques for multiresolution structures.

Wriggers W, Chacón P.

Structure. 2001 Sep;9(9):779-88. No abstract available.

50.

Using situs for flexible and rigid-body fitting of multiresolution single-molecule data.

Wriggers W, Birmanns S.

J Struct Biol. 2001 Feb-Mar;133(2-3):193-202.

PMID:
11472090

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