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Items: 1 to 50 of 58

1.

Tissue and cellular mechanics of seeds.

Steinbrecher T, Leubner-Metzger G.

Curr Opin Genet Dev. 2018 Mar 20;51:1-10. doi: 10.1016/j.gde.2018.03.001. [Epub ahead of print] Review.

2.

Finite indentation of highly curved elastic shells.

Pearce SP, King JR, Steinbrecher T, Leubner-Metzger G, Everitt NM, Holdsworth MJ.

Proc Math Phys Eng Sci. 2018 Jan;474(2209):20170482. doi: 10.1098/rspa.2017.0482. Epub 2018 Jan 24.

3.

Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors.

Orgován Z, Ferenczy GG, Steinbrecher T, Szilágyi B, Bajusz D, Keserű GM.

J Comput Aided Mol Des. 2018 Feb;32(2):331-345. doi: 10.1007/s10822-018-0097-y. Epub 2018 Jan 15.

PMID:
29335871
4.

Fruit fracture biomechanics and the release of Lepidium didymum pericarp-imposed mechanical dormancy by fungi.

Sperber K, Steinbrecher T, Graeber K, Scherer G, Clausing S, Wiegand N, Hourston JE, Kurre R, Leubner-Metzger G, Mummenhoff K.

Nat Commun. 2017 Nov 30;8(1):1868. doi: 10.1038/s41467-017-02051-9.

5.

A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases.

Bertoldo JB, Rodrigues T, Dunsmore L, Aprile FA, Marques MC, Rosado LA, Boutureira O, Steinbrecher TB, Sherman W, Corzana F, Terenzi H, Bernardes GJL.

Chem. 2017 Oct 12;3(4):665-677. doi: 10.1016/j.chempr.2017.07.009.

6.

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions.

Jacobson LD, Bochevarov AD, Watson MA, Hughes TF, Rinaldo D, Ehrlich S, Steinbrecher TB, Vaitheeswaran S, Philipp DM, Halls MD, Friesner RA.

J Chem Theory Comput. 2017 Nov 14;13(11):5780-5797. doi: 10.1021/acs.jctc.7b00764. Epub 2017 Oct 17.

PMID:
28957627
7.

Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations.

Steinbrecher T, Abel R, Clark A, Friesner R.

J Mol Biol. 2017 Apr 7;429(7):923-929. doi: 10.1016/j.jmb.2017.03.002. Epub 2017 Mar 6.

PMID:
28279701
8.

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study.

Keränen H, Pérez-Benito L, Ciordia M, Delgado F, Steinbrecher TB, Oehlrich D, van Vlijmen HW, Trabanco AA, Tresadern G.

J Chem Theory Comput. 2017 Mar 14;13(3):1439-1453. doi: 10.1021/acs.jctc.6b01141. Epub 2017 Feb 3.

PMID:
28103438
9.

Biomechanical properties of wheat grains: the implications on milling.

Hourston JE, Ignatz M, Reith M, Leubner-Metzger G, Steinbrecher T.

J R Soc Interface. 2017 Jan;14(126). pii: 20160828. doi: 10.1098/rsif.2016.0828.

10.

Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability-Large-Scale Validation of MD-Based Relative Free Energy Calculations.

Steinbrecher T, Zhu C, Wang L, Abel R, Negron C, Pearlman D, Feyfant E, Duan J, Sherman W.

J Mol Biol. 2017 Apr 7;429(7):948-963. doi: 10.1016/j.jmb.2016.12.007. Epub 2016 Dec 10.

PMID:
27964946
11.

The biomechanics of seed germination.

Steinbrecher T, Leubner-Metzger G.

J Exp Bot. 2017 Feb 1;68(4):765-783. doi: 10.1093/jxb/erw428. Review.

PMID:
27927995
12.

Developmental Control and Plasticity of Fruit and Seed Dimorphism in Aethionema arabicum.

Lenser T, Graeber K, Cevik ÖS, Adigüzel N, Dönmez AA, Grosche C, Kettermann M, Mayland-Quellhorst S, Mérai Z, Mohammadin S, Nguyen TP, Rümpler F, Schulze C, Sperber K, Steinbrecher T, Wiegand N, Strnad M, Scheid OM, Rensing SA, Schranz ME, Theißen G, Mummenhoff K, Leubner-Metzger G.

Plant Physiol. 2016 Nov;172(3):1691-1707. Epub 2016 Oct 4.

13.

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, van den Broek K, Epple M, Kuhn H, Truszkowski A, Zielesny A, Fraaije JH, Gracia RS, Kast SM, Bulusu KC, Bender A, Yosipof A, Nahum O, Senderowitz H, Krotzky T, Schulz R, Wolber G, Bietz S, Rarey M, Zimmermann MO, Lange A, Ruff M, Heidrich J, Onlia I, Exner TE, Boeckler FM, Bermudez M, Firaha DS, Hollóczki O, Kirchner B, Tautermann CS, Volkamer A, Eid S, Turk S, Rippmann F, Fulle S, Saleh N, Saladino G, Gervasio FL, Haensele E, Banting L, Whitley DC, Oliveira Santos JS, Bureau R, Clark T, Sandmann A, Lanig H, Kibies P, Heil J, Hoffgaard F, Frach R, Engel J, Smith S, Basu D, Rauh D, Kohlbacher O, Boeckler FM, Essex JW, Bodnarchuk MS, Ross GA, Finkelmann AR, Göller AH, Schneider G, Husch T, Schütter C, Balducci A, Korth M, Ntie-Kang F, Günther S, Sippl W, Mbaze LM, Ntie-Kang F, Simoben CV, Lifongo LL, Ntie-Kang F, Judson P, Barilla J, Lokajíček MV, Pisaková H, Simr P, Kireeva N, Petrov A, Ostroumov D, Solovev VP, Pervov VS, Friedrich NO, Sommer K, Rarey M, Kirchmair J, Proschak E, Weber J, Moser D, Kalinowski L, Achenbach J, Mackey M, Cheeseright T, Renner G, Renner G, Schmidt TC, Schram J, Egelkraut-Holtus M, van Oeyen A, Kalliokoski T, Fourches D, Ibezim A, Mbah CJ, Adikwu UM, Nwodo NJ, Steudle A, Masek BB, Nagy S, Baker D, Soltanshahi F, Dorfman R, Dubrucq K, Patel H, Koch O, Mrugalla F, Kast SM, Ain QU, Fuchs JE, Owen RM, Omoto K, Torella R, Pryde DC, Glen R, Bender A, Hošek P, Spiwok V, Mervin LH, Barrett I, Firth M, Murray DC, McWilliams L, Cao Q, Engkvist O, Warszycki D, Śmieja M, Bojarski AJ, Aniceto N, Freitas A, Ghafourian T, Herrmann G, Eigner-Pitto V, Naß A, Kurczab R, Bojarski AJ, Lange A, Günther MB, Hennig S, Büttner FM, Schall C, Sievers-Engler A, Ansideri F, Koch P, Stehle T, Laufer S, Böckler FM, Zdrazil B, Montanari F, Ecker GF, Grebner C, Hogner A, Ulander J, Edman K, Guallar V, Tyrchan C, Ulander J, Tyrchan C, Klute W, Bergström F, Kramer C, Nguyen QD, Frach R, Kibies P, Strohfeldt S, Böttcher S, Pongratz T, Horinek D, Kast SM, Rupp B, Al-Yamori R, Lisurek M, Kühne R, Furtado F, van den Broek K, Wessjohann L, Mathea M, Baumann K, Mohamad-Zobir SZ, Fu X, Fan TP, Bender A, Kuhn MA, Sotriffer CA, Zoufir A, Li X, Mervin L, Berg E, Polokoff M, Ihlenfeldt WD, Ihlenfeldt WD, Pretzel J, Alhalabi Z, Fraczkiewicz R, Waldman M, Clark RD, Shaikh N, Garg P, Kos A, Himmler HJ, Sandmann A, Jardin C, Sticht H, Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W, Pöhner IA, Panecka J, Wade RC, Bietz S, Schomburg KT, Hilbig M, Rarey M, Jäger C, Wieczorek V, Westerhoff LM, Borbulevych OY, Demuth HU, Buchholz M, Schmidt D, Rickmeyer T, Krotzky T, Kolb P, Mittal S, Sánchez-García E, Nogueira MS, Oliveira TB, da Costa FB, Schmidt TJ.

J Cheminform. 2016 Apr 26;8(Suppl 1):18. doi: 10.1186/s13321-016-0119-5. No abstract available.

14.

A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes.

Leonis G, Avramopoulos A, Papavasileiou KD, Reis H, Steinbrecher T, Papadopoulos MG.

J Phys Chem B. 2015 Dec 3;119(48):14971-85. doi: 10.1021/acs.jpcb.5b05998. Epub 2015 Nov 18.

PMID:
26523956
15.

Accurate Binding Free Energy Predictions in Fragment Optimization.

Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W.

J Chem Inf Model. 2015 Nov 23;55(11):2411-20. doi: 10.1021/acs.jcim.5b00538. Epub 2015 Oct 21.

PMID:
26457994
16.

Stereoselective synthesis and molecular modeling of chiral cyclopentanes.

Abdel-Jalil RJ, Steinbrecher T, Al-Harthy T, Mahal A, Abou-Zied OK, Voelter W.

Carbohydr Res. 2015 Oct 13;415:12-6. doi: 10.1016/j.carres.2015.07.012. Epub 2015 Jul 23.

PMID:
26267888
17.

Pyrido[4,3-e][1,2,4]triazolo[4,3-a]pyrazines as Selective, Brain Penetrant Phosphodiesterase 2 (PDE2) Inhibitors.

Rombouts FJ, Tresadern G, Buijnsters P, Langlois X, Tovar F, Steinbrecher TB, Vanhoof G, Somers M, Andrés JI, Trabanco AA.

ACS Med Chem Lett. 2015 Jan 15;6(3):282-6. doi: 10.1021/ml500463t. eCollection 2015 Mar 12.

18.

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.

Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R.

J Am Chem Soc. 2015 Feb 25;137(7):2695-703. doi: 10.1021/ja512751q. Epub 2015 Feb 12.

PMID:
25625324
19.

DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination.

Graeber K, Linkies A, Steinbrecher T, Mummenhoff K, Tarkowská D, Turečková V, Ignatz M, Sperber K, Voegele A, de Jong H, Urbanová T, Strnad M, Leubner-Metzger G.

Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):E3571-80. doi: 10.1073/pnas.1403851111. Epub 2014 Aug 11.

20.

3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides.

Reißer S, Strandberg E, Steinbrecher T, Ulrich AS.

Biophys J. 2014 Jun 3;106(11):2385-94. doi: 10.1016/j.bpj.2014.04.020.

21.

Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

Wolter T, Steinbrecher T, Trauner D, Elstner M.

PLoS One. 2014 Apr 8;9(4):e92716. doi: 10.1371/journal.pone.0092716. eCollection 2014.

22.

Fragment orbital based description of charge transfer in peptides including backbone orbitals.

Heck A, Woiczikowski PB, Kubař T, Welke K, Niehaus T, Giese B, Skourtis S, Elstner M, Steinbrecher TB.

J Phys Chem B. 2014 Apr 24;118(16):4261-72. doi: 10.1021/jp408907g. Epub 2014 Apr 11.

PMID:
24655342
23.

Controlling biological activity with light: diarylethene-containing cyclic peptidomimetics.

Babii O, Afonin S, Berditsch M, Reiβer S, Mykhailiuk PK, Kubyshkin VS, Steinbrecher T, Ulrich AS, Komarov IV.

Angew Chem Int Ed Engl. 2014 Mar 24;53(13):3392-5. doi: 10.1002/anie.201310019. Epub 2014 Feb 19.

PMID:
24554486
24.

Ground state spectroscopy of hydroxyquinolines: evidence for the formation of protonated species in water-rich dioxane-water mixtures.

Abou-Zied OK, Husband J, Al-Lawatia N, Steinbrecher TB.

Phys Chem Chem Phys. 2014 Jan 7;16(1):61-70. doi: 10.1039/c3cp52811a.

PMID:
24158492
25.

Charge transfer in E. coli DNA photolyase: understanding polarization and stabilization effects via QM/MM simulations.

Lüdemann G, Woiczikowski PB, Kubař T, Elstner M, Steinbrecher TB.

J Phys Chem B. 2013 Sep 19;117(37):10769-78. doi: 10.1021/jp406319b. Epub 2013 Sep 4.

PMID:
23964783
26.
27.

Computational study of synthetic agonist ligands of ionotropic glutamate receptors.

Wolter T, Steinbrecher T, Elstner M.

PLoS One. 2013;8(3):e58774. doi: 10.1371/journal.pone.0058774. Epub 2013 Mar 25.

28.

Binding of hydroxyquinoline probes to human serum albumin: combining molecular modeling and Förster's resonance energy transfer spectroscopy to understand flexible ligand binding.

Abou-Zied OK, Al-Lawatia N, Elstner M, Steinbrecher TB.

J Phys Chem B. 2013 Jan 31;117(4):1062-74. doi: 10.1021/jp311238n. Epub 2013 Jan 22.

PMID:
23297700
29.

Revised AMBER parameters for bioorganic phosphates.

Steinbrecher T, Latzer J, Case DA.

J Chem Theory Comput. 2012 Nov 13;8(11):4405-4412. Epub 2012 Sep 12.

30.

Peptide-lipid interactions of the stress-response peptide TisB that induces bacterial persistence.

Steinbrecher T, Prock S, Reichert J, Wadhwani P, Zimpfer B, Bürck J, Berditsch M, Elstner M, Ulrich AS.

Biophys J. 2012 Oct 3;103(7):1460-9. doi: 10.1016/j.bpj.2012.07.060. Epub 2012 Oct 2.

31.

QM and QM/MM simulations of proteins.

Steinbrecher T, Elstner M.

Methods Mol Biol. 2013;924:91-124. doi: 10.1007/978-1-62703-017-5_5. Review.

PMID:
23034747
32.

Rotamer decomposition and protein dynamics: efficiently analyzing dihedral populations from molecular dynamics.

Watanabe H, Elstner M, Steinbrecher T.

J Comput Chem. 2013 Jan 30;34(3):198-205. doi: 10.1002/jcc.23119. Epub 2012 Sep 25.

PMID:
23007849
33.

Distinct cell wall architectures in seed endosperms in representatives of the Brassicaceae and Solanaceae.

Lee KJ, Dekkers BJ, Steinbrecher T, Walsh CT, Bacic A, Bentsink L, Leubner-Metzger G, Knox JP.

Plant Physiol. 2012 Nov;160(3):1551-66. doi: 10.1104/pp.112.203661. Epub 2012 Sep 6.

34.

Fascaplysin as a specific inhibitor for CDK4: insights from molecular modelling.

Shafiq MI, Steinbrecher T, Schmid R.

PLoS One. 2012;7(8):e42612. doi: 10.1371/journal.pone.0042612. Epub 2012 Aug 14.

35.

Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I.

Steinbrecher T, Case DA, Labahn A.

Bioorg Med Chem. 2012 Jun 1;20(11):3446-53. doi: 10.1016/j.bmc.2012.04.019. Epub 2012 Apr 16.

PMID:
22560835
36.

Recent progress in biological charge transfer: theory and simulation.

Koslowski T, Burggraf F, Krapf S, Steinbrecher T, Wittekindt C.

Biochim Biophys Acta. 2012 Oct;1817(10):1955-7. doi: 10.1016/j.bbabio.2012.02.025. Epub 2012 Feb 28.

37.

Free energy calculations on snake venom metalloproteinase BaP1.

Lingott T, Merfort I, Steinbrecher T.

Chem Biol Drug Des. 2012 Jun;79(6):990-1000. doi: 10.1111/j.1747-0285.2012.01369.x. Epub 2012 Apr 17.

PMID:
22385614
38.

Molecular origin of differences in hole and electron mobility in amorphous Alq3--a multiscale simulation study.

Fuchs A, Steinbrecher T, Mommer MS, Nagata Y, Elstner M, Lennartz C.

Phys Chem Chem Phys. 2012 Mar 28;14(12):4259-70. doi: 10.1039/c2cp23489k. Epub 2012 Feb 15.

PMID:
22337316
39.

Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation.

Heck A, Woiczikowski PB, Kubař T, Giese B, Elstner M, Steinbrecher TB.

J Phys Chem B. 2012 Feb 23;116(7):2284-93. doi: 10.1021/jp2086297. Epub 2012 Feb 9.

PMID:
22260641
40.

Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations.

Steinbrecher T, Joung I, Case DA.

J Comput Chem. 2011 Nov 30;32(15):3253-63. doi: 10.1002/jcc.21909. Epub 2011 Aug 27.

41.

Structure, attachment properties, and ecological importance of the attachment system of English ivy (Hedera helix).

Melzer B, Seidel R, Steinbrecher T, Speck T.

J Exp Bot. 2012 Jan;63(1):191-201. doi: 10.1093/jxb/err260. Epub 2011 Sep 13.

42.

Nonadiabatic QM/MM simulations of fast charge transfer in Escherichia coli DNA photolyase.

Woiczikowski PB, Steinbrecher T, Kubař T, Elstner M.

J Phys Chem B. 2011 Aug 18;115(32):9846-63. doi: 10.1021/jp204696t. Epub 2011 Jul 27.

PMID:
21793510
43.

Tautomerism in 7-hydroxyquinoline: a combined experimental and theoretical study in water.

Al-Lawatia N, Husband J, Steinbrecher T, Abou-Zied OK.

J Phys Chem A. 2011 May 5;115(17):4195-201. doi: 10.1021/jp201649z. Epub 2011 Apr 8.

PMID:
21476526
44.

The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions.

Krapf S, Koslowski T, Steinbrecher T.

Phys Chem Chem Phys. 2010 Aug 28;12(32):9516-25. doi: 10.1039/c000876a. Epub 2010 Jun 8.

PMID:
20532362
45.

The attachment strategy of English ivy: a complex mechanism acting on several hierarchical levels.

Melzer B, Steinbrecher T, Seidel R, Kraft O, Schwaiger R, Speck T.

J R Soc Interface. 2010 Sep 6;7(50):1383-9. doi: 10.1098/rsif.2010.0140. Epub 2010 May 12.

46.

Towards accurate free energy calculations in ligand protein-binding studies.

Steinbrecher T, Labahn A.

Curr Med Chem. 2010;17(8):767-85. Review.

PMID:
20088755
47.

Quantifying the attachment strength of climbing plants: a new approach.

Steinbrecher T, Danninger E, Harder D, Speck T, Kraft O, Schwaiger R.

Acta Biomater. 2010 Apr;6(4):1497-504. doi: 10.1016/j.actbio.2009.10.003. Epub 2009 Oct 8.

PMID:
19818882
48.

Direct simulation of electron transfer reactions in DNA radical cations.

Steinbrecher T, Koslowski T, Case DA.

J Phys Chem B. 2008 Dec 25;112(51):16935-44. doi: 10.1021/jp8076134.

49.

Bornyl (3,4,5-trihydroxy)-cinnamate--an optimized human neutrophil elastase inhibitor designed by free energy calculations.

Steinbrecher T, Hrenn A, Dormann KL, Merfort I, Labahn A.

Bioorg Med Chem. 2008 Mar 1;16(5):2385-90. Epub 2007 Nov 29.

PMID:
18078761
50.

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

Steinbrecher T, Mobley DL, Case DA.

J Chem Phys. 2007 Dec 7;127(21):214108.

PMID:
18067350

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