Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 35

1.

Simulation of FRET dyes allows quantitative comparison against experimental data.

Reinartz I, Sinner C, Nettels D, Stucki-Buchli B, Stockmar F, Panek PT, Jacob CR, Nienhaus GU, Schuler B, Schug A.

J Chem Phys. 2018 Mar 28;148(12):123321. doi: 10.1063/1.5010434.

PMID:
29604831
2.

Biomolecular coevolution and its applications: Going from structure prediction toward signaling, epistasis, and function.

Zerihun MB, Schug A.

Biochem Soc Trans. 2017 Dec 15;45(6):1253-1261. doi: 10.1042/BST20170063. Epub 2017 Oct 20. Review.

PMID:
29054926
3.

Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis.

Uguzzoni G, John Lovis S, Oteri F, Schug A, Szurmant H, Weigt M.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2662-E2671. doi: 10.1073/pnas.1615068114. Epub 2017 Mar 13.

4.

Revealing the global map of protein folding space by large-scale simulations.

Sinner C, Lutz B, Verma A, Schug A.

J Chem Phys. 2015 Dec 28;143(24):243154. doi: 10.1063/1.4938172.

PMID:
26723639
5.

Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures.

Lammert H, Noel JK, Haglund E, Schug A, Onuchic JN.

J Chem Phys. 2015 Dec 28;143(24):243141. doi: 10.1063/1.4936881.

PMID:
26723626
6.

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1.

Figliuzzi M, Jacquier H, Schug A, Tenaillon O, Weigt M.

Mol Biol Evol. 2016 Jan;33(1):268-80. doi: 10.1093/molbev/msv211. Epub 2015 Oct 6.

7.

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction.

De Leonardis E, Lutz B, Ratz S, Cocco S, Monasson R, Schug A, Weigt M.

Nucleic Acids Res. 2015 Dec 2;43(21):10444-55. doi: 10.1093/nar/gkv932. Epub 2015 Sep 29.

8.

Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY.

Methods Enzymol. 2015;553:215-34. doi: 10.1016/bs.mie.2014.10.061. Epub 2015 Feb 7.

9.

Filopodia-based Wnt transport during vertebrate tissue patterning.

Stanganello E, Hagemann AI, Mattes B, Sinner C, Meyen D, Weber S, Schug A, Raz E, Scholpp S.

Nat Commun. 2015 Jan 5;6:5846. doi: 10.1038/ncomms6846.

PMID:
25556612
10.

Argon: systematic review on neuro- and organoprotective properties of an "inert" gas.

Höllig A, Schug A, Fahlenkamp AV, Rossaint R, Coburn M; Argon Organo-Protective Network (AON).

Int J Mol Sci. 2014 Oct 10;15(10):18175-96. doi: 10.3390/ijms151018175. Review.

11.

Native structure-based modeling and simulation of biomolecular systems per mouse click.

Lutz B, Sinner C, Bozic S, Kondov I, Schug A.

BMC Bioinformatics. 2014 Aug 29;15:292. doi: 10.1186/1471-2105-15-292.

12.

Differences between cotranscriptional and free riboswitch folding.

Lutz B, Faber M, Verma A, Klumpp S, Schug A.

Nucleic Acids Res. 2014 Feb;42(4):2687-96. doi: 10.1093/nar/gkt1213. Epub 2013 Nov 25.

13.

eSBMTools 1.0: enhanced native structure-based modeling tools.

Lutz B, Sinner C, Heuermann G, Verma A, Schug A.

Bioinformatics. 2013 Nov 1;29(21):2795-6. doi: 10.1093/bioinformatics/btt478. Epub 2013 Sep 9.

PMID:
24021379
14.

Structure based design of protein linkers for zinc finger nuclease.

Anand P, Schug A, Wenzel W.

FEBS Lett. 2013 Oct 1;587(19):3231-5. doi: 10.1016/j.febslet.2013.08.015. Epub 2013 Aug 27.

15.

Modulation of a pre-existing conformational equilibrium tunes adenylate kinase activity.

Ådén J, Verma A, Schug A, Wolf-Watz M.

J Am Chem Soc. 2012 Oct 10;134(40):16562-70. doi: 10.1021/ja3032482. Epub 2012 Sep 25.

PMID:
22963267
16.

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis.

Dago AE, Schug A, Procaccini A, Hoch JA, Weigt M, Szurmant H.

Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1733-42. doi: 10.1073/pnas.1201301109. Epub 2012 Jun 5.

17.

Mirror images as naturally competing conformations in protein folding.

Noel JK, Schug A, Verma A, Wenzel W, Garcia AE, Onuchic JN.

J Phys Chem B. 2012 Jun 14;116(23):6880-8. doi: 10.1021/jp212623d. Epub 2012 Apr 26.

PMID:
22497217
18.

Allostery in the ferredoxin protein motif does not involve a conformational switch.

Nechushtai R, Lammert H, Michaeli D, Eisenberg-Domovich Y, Zuris JA, Luca MA, Capraro DT, Fish A, Shimshon O, Roy M, Schug A, Whitford PC, Livnah O, Onuchic JN, Jennings PA.

Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2240-5. doi: 10.1073/pnas.1019502108. Epub 2011 Jan 25.

19.

From protein folding to protein function and biomolecular binding by energy landscape theory.

Schug A, Onuchic JN.

Curr Opin Pharmacol. 2010 Dec;10(6):709-14. doi: 10.1016/j.coph.2010.09.012. Epub 2010 Oct 14. Review.

PMID:
20951644
20.

Computational modeling of phosphotransfer complexes in two-component signaling.

Schug A, Weigt M, Hoch JA, Onuchic JN, Hwa T, Szurmant H.

Methods Enzymol. 2010;471:43-58. doi: 10.1016/S0076-6879(10)71003-X. Epub 2010 Mar 1.

PMID:
20946841
21.

High-resolution protein complexes from integrating genomic information with molecular simulation.

Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H.

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22124-9. doi: 10.1073/pnas.0912100106. Epub 2009 Dec 17.

22.

Robustness and generalization of structure-based models for protein folding and function.

Lammert H, Schug A, Onuchic JN.

Proteins. 2009 Dec;77(4):881-91. doi: 10.1002/prot.22511.

PMID:
19626713
23.

Direct single-molecule observation of a protein living in two opposed native structures.

Gambin Y, Schug A, Lemke EA, Lavinder JJ, Ferreon AC, Magliery TJ, Onuchic JN, Deniz AA.

Proc Natl Acad Sci U S A. 2009 Jun 23;106(25):10153-8. doi: 10.1073/pnas.0904461106. Epub 2009 Jun 8.

24.

All-atom protein folding with free-energy forcefields.

Verma A, Gopal SM, Schug A, Herges T, Klenin K, Wenzel W.

Prog Mol Biol Transl Sci. 2008;83:181-253. doi: 10.1016/S0079-6603(08)00605-3. Review. No abstract available.

PMID:
19186255
25.

Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function.

Whitford PC, Schug A, Saunders J, Hennelly SP, Onuchic JN, Sanbonmatsu KY.

Biophys J. 2009 Jan;96(2):L7-9. doi: 10.1016/j.bpj.2008.10.033.

26.

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

Whitford PC, Noel JK, Gosavi S, Schug A, Sanbonmatsu KY, Onuchic JN.

Proteins. 2009 May 1;75(2):430-41. doi: 10.1002/prot.22253.

27.

Geometrical features of the protein folding mechanism are a robust property of the energy landscape: a detailed investigation of several reduced models.

Oliveira LC, Schug A, Onuchic JN.

J Phys Chem B. 2008 May 15;112(19):6131-6. doi: 10.1021/jp0769835. Epub 2008 Feb 6.

PMID:
18251535
28.

Mutations as trapdoors to two competing native conformations of the Rop-dimer.

Schug A, Whitford PC, Levy Y, Onuchic JN.

Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17674-9. Epub 2007 Oct 29.

29.

An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein l20.

Schug A, Wenzel W.

Biophys J. 2006 Jun 15;90(12):4273-80. Epub 2006 Mar 24.

30.

Basin hopping simulations for all-atom protein folding.

Verma A, Schug A, Lee KH, Wenzel W.

J Chem Phys. 2006 Jan 28;124(4):044515.

PMID:
16460193
31.

Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.

Schug A, Herges T, Verma A, Lee KH, Wenzel W.

Chemphyschem. 2005 Dec 9;6(12):2640-6.

PMID:
16331731
32.

Energy landscape paving simulations of the trp-cage protein.

Schug A, Wenzel W, Hansmann UH.

J Chem Phys. 2005 May 15;122(19):194711.

PMID:
16161610
33.

Predictive in silico all-atom folding of a four-helix protein with a free-energy model.

Schug A, Wenzel W.

J Am Chem Soc. 2004 Dec 29;126(51):16736-7.

PMID:
15612707
34.
35.

Reproducible protein folding with the stochastic tunneling method.

Schug A, Herges T, Wenzel W.

Phys Rev Lett. 2003 Oct 10;91(15):158102. Epub 2003 Oct 6.

PMID:
14611501

Supplemental Content

Support Center