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Items: 1 to 50 of 66

1.

Metadynamics to Enhance Sampling in Biomolecular Simulations.

Pfaendtner J.

Methods Mol Biol. 2019;2022:179-200. doi: 10.1007/978-1-4939-9608-7_8.

PMID:
31396904
2.

Trimethylamine N-oxide-derived zwitterionic polymers: A new class of ultralow fouling bioinspired materials.

Li B, Jain P, Ma J, Smith JK, Yuan Z, Hung HC, He Y, Lin X, Wu K, Pfaendtner J, Jiang S.

Sci Adv. 2019 Jun 14;5(6):eaaw9562. doi: 10.1126/sciadv.aaw9562. eCollection 2019 Jun.

3.

Assessment of molecular dynamics simulations for amorphous poly(3-hexylthiophene) using neutron and X-ray scattering experiments.

Wolf CM, Kanekal KH, Yimer YY, Tyagi M, Omar-Diallo S, Pakhnyuk V, Luscombe CK, Pfaendtner J, Pozzo LD.

Soft Matter. 2019 Jun 26;15(25):5067-5083. doi: 10.1039/c9sm00807a.

PMID:
31183486
4.

Fantastic Liquids and Where To Find Them: Optimizations of Discrete Chemical Space.

Beckner W, Pfaendtner J.

J Chem Inf Model. 2019 Jun 24;59(6):2617-2625. doi: 10.1021/acs.jcim.9b00087. Epub 2019 Apr 19.

PMID:
30974059
5.

Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces.

Mao CM, Sampath J, Sprenger KG, Drobny G, Pfaendtner J.

Langmuir. 2019 Apr 30;35(17):5911-5920. doi: 10.1021/acs.langmuir.8b01392. Epub 2019 Apr 22.

PMID:
30955325
6.

Diagnosing the Impact of External Electric Fields Chemical Kinetics: Application to Toluene Oxidation and Pyrolysis.

Fu CD, He Y, Pfaendtner J.

J Phys Chem A. 2019 Apr 11;123(14):3080-3089. doi: 10.1021/acs.jpca.8b11780. Epub 2019 Mar 28.

PMID:
30843399
7.

Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces.

Buckle EL, Prakash A, Bonomi M, Sampath J, Pfaendtner J, Drobny GP.

J Am Chem Soc. 2019 Feb 6;141(5):1998-2011. doi: 10.1021/jacs.8b10990. Epub 2019 Jan 24.

PMID:
30618247
8.

Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water.

Verreault D, Alamdari S, Roeters SJ, Pandey R, Pfaendtner J, Weidner T.

Phys Chem Chem Phys. 2018 Oct 31;20(42):26926-26933. doi: 10.1039/c8cp03382j.

PMID:
30260363
9.

Inhibition of the Exoglucanase Cel7A by a Douglas-Fir-Condensed Tannin.

Oleson KR, Sprenger KG, Pfaendtner J, Schwartz DT.

J Phys Chem B. 2018 Sep 20;122(37):8665-8674. doi: 10.1021/acs.jpcb.8b05850. Epub 2018 Sep 10.

PMID:
30111095
10.

Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics.

Prakash A, Fu CD, Bonomi M, Pfaendtner J.

J Chem Theory Comput. 2018 Oct 9;14(10):4985-4990. doi: 10.1021/acs.jctc.8b00448. Epub 2018 Sep 6.

PMID:
30075630
11.

Density functional tight-binding and infrequent metadynamics can capture entropic effects in intramolecular hydrogen transfer reactions.

Oliveira LFL, Fu CD, Pfaendtner J.

J Chem Phys. 2018 Apr 21;148(15):154101. doi: 10.1063/1.5021359.

PMID:
29679963
12.

Lifting the Curse of Dimensionality on Enhanced Sampling of Reaction Networks with Parallel Bias Metadynamics.

Fu CD, Pfaendtner J.

J Chem Theory Comput. 2018 May 8;14(5):2516-2525. doi: 10.1021/acs.jctc.7b01289. Epub 2018 Apr 18.

PMID:
29608848
13.

Design of Polyphosphate Inhibitors: A Molecular Dynamics Investigation on Polyethylene Glycol-Linked Cationic Binding Groups.

Mafi A, Abbina S, Kalathottukaren MT, Morrissey JH, Haynes C, Kizhakkedathu JN, Pfaendtner J, Chou KC.

Biomacromolecules. 2018 Apr 9;19(4):1358-1367. doi: 10.1021/acs.biomac.8b00327. Epub 2018 Mar 23.

14.

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation.

Prakash A, Baer MD, Mundy CJ, Pfaendtner J.

Biomacromolecules. 2018 Mar 12;19(3):1006-1015. doi: 10.1021/acs.biomac.7b01813. Epub 2018 Feb 27.

PMID:
29443506
15.

Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids.

Summers SR, Sprenger KG, Pfaendtner J, Marchant J, Summers MF, Kaar JL.

J Phys Chem B. 2017 Dec 7;121(48):10793-10803. doi: 10.1021/acs.jpcb.7b08435. Epub 2017 Nov 21.

PMID:
29120187
16.

LK peptide side chain dynamics at interfaces are independent of secondary structure.

Donovan MA, Lutz H, Yimer YY, Pfaendtner J, Bonn M, Weidner T.

Phys Chem Chem Phys. 2017 Nov 1;19(42):28507-28511. doi: 10.1039/c7cp05897g.

PMID:
29043310
17.

Investigating the Role of Phosphorylation in the Binding of Silaffin Peptide R5 to Silica with Molecular Dynamics Simulations.

Sprenger KG, Prakash A, Drobny G, Pfaendtner J.

Langmuir. 2018 Jan 23;34(3):1199-1207. doi: 10.1021/acs.langmuir.7b02868. Epub 2017 Oct 24.

PMID:
28981294
18.

Redefining the Protein-Protein Interface: Coarse Graining and Combinatorics for an Improved Understanding of Amino Acid Contributions to the Protein-Protein Binding Affinity.

Smith JK, Jiang S, Pfaendtner J.

Langmuir. 2017 Oct 24;33(42):11511-11517. doi: 10.1021/acs.langmuir.7b02438. Epub 2017 Sep 12.

PMID:
28850233
19.

Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation.

Prakash A, Sprenger KG, Pfaendtner J.

Biochem Biophys Res Commun. 2018 Mar 29;498(2):274-281. doi: 10.1016/j.bbrc.2017.07.066. Epub 2017 Jul 15.

PMID:
28720500
20.

Elucidating sequence and solvent specific design targets to protect and stabilize enzymes for biocatalysis in ionic liquids.

Sprenger KG, Plaks JG, Kaar JL, Pfaendtner J.

Phys Chem Chem Phys. 2017 Jul 5;19(26):17426-17433. doi: 10.1039/c7cp03013d.

PMID:
28650512
21.

The Structure of the Diatom Silaffin Peptide R5 within Freestanding Two-Dimensional Biosilica Sheets.

Lutz H, Jaeger V, Schmüser L, Bonn M, Pfaendtner J, Weidner T.

Angew Chem Int Ed Engl. 2017 Jul 3;56(28):8277-8280. doi: 10.1002/anie.201702707. Epub 2017 Jun 13.

PMID:
28608998
22.

Determining dominant driving forces affecting controlled protein release from polymeric nanoparticles.

Smith J, Sprenger KG, Liao R, Joseph A, Nance E, Pfaendtner J.

Biointerphases. 2017 May 19;12(2):02D412. doi: 10.1116/1.4983154.

23.

Enhancing the Oxidation of Toluene with External Electric Fields: a Reactive Molecular Dynamics Study.

Tan S, Xia T, Shi Y, Pfaendtner J, Zhao S, He Y.

Sci Rep. 2017 May 10;7(1):1710. doi: 10.1038/s41598-017-01945-4.

24.

Tuning crystallization pathways through sequence engineering of biomimetic polymers.

Ma X, Zhang S, Jiao F, Newcomb CJ, Zhang Y, Prakash A, Liao Z, Baer MD, Mundy CJ, Pfaendtner J, Noy A, Chen CL, De Yoreo JJ.

Nat Mater. 2017 Jul;16(7):767-774. doi: 10.1038/nmat4891. Epub 2017 Apr 17.

PMID:
28414316
25.

Assessing Generic Collective Variables for Determining Reaction Rates in Metadynamics Simulations.

Fu CD, Oliveira LF, Pfaendtner J.

J Chem Theory Comput. 2017 Mar 14;13(3):968-973. doi: 10.1021/acs.jctc.7b00038. Epub 2017 Feb 22.

PMID:
28212010
26.

Determining energy barriers and selectivities of a multi-pathway system with infrequent metadynamics.

Fu CD, L Oliveira LF, Pfaendtner J.

J Chem Phys. 2017 Jan 7;146(1):014108. doi: 10.1063/1.4971800.

PMID:
28063430
27.

Acetylation dictates the morphology of nanophase biosilica precipitated by a 14-amino acid leucine-lysine peptide.

Lutz H, Jaeger V, Bonn M, Pfaendtner J, Weidner T.

J Pept Sci. 2017 Feb;23(2):141-147. doi: 10.1002/psc.2960. Epub 2016 Dec 28.

PMID:
28028919
28.

Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations.

Jaeger VW, Pfaendtner J.

J Phys Chem B. 2016 Dec 1;120(47):12079-12087. Epub 2016 Nov 21.

PMID:
27809527
29.

Chain Flexibility in Self-Assembled Monolayers Affects Protein Adsorption and Surface Hydration: A Molecular Dynamics Study.

Beckner W, He Y, Pfaendtner J.

J Phys Chem B. 2016;120(40):10423-10432. Epub 2016 Oct 4.

PMID:
27643945
30.

Using Molecular Simulation to Study Biocatalysis in Ionic Liquids.

Sprenger KG, Pfaendtner J.

Methods Enzymol. 2016;577:419-41. doi: 10.1016/bs.mie.2016.05.020. Epub 2016 Jun 28.

PMID:
27498647
31.

Strong Electrostatic Interactions Lead to Entropically Favorable Binding of Peptides to Charged Surfaces.

Sprenger KG, Pfaendtner J.

Langmuir. 2016 Jun 7;32(22):5690-701. doi: 10.1021/acs.langmuir.6b01296. Epub 2016 May 24.

PMID:
27181161
32.

Ice-nucleating bacteria control the order and dynamics of interfacial water.

Pandey R, Usui K, Livingstone RA, Fischer SA, Pfaendtner J, Backus EH, Nagata Y, Fröhlich-Nowoisky J, Schmüser L, Mauri S, Scheel JF, Knopf DA, Pöschl U, Bonn M, Weidner T.

Sci Adv. 2016 Apr 22;2(4):e1501630. doi: 10.1126/sciadv.1501630. eCollection 2016 Apr.

33.

Ultrafast Reorientational Dynamics of Leucine at the Air-Water Interface.

Donovan MA, Yimer YY, Pfaendtner J, Backus EH, Bonn M, Weidner T.

J Am Chem Soc. 2016 Apr 27;138(16):5226-9. doi: 10.1021/jacs.6b01878. Epub 2016 Apr 18.

PMID:
27057584
34.

Lytic Polysaccharide Monooxygenases ScLPMO10B and ScLPMO10C Are Stable in Ionic Liquids As Determined by Molecular Simulations.

Sprenger KG, Choudhury A, Kaar JL, Pfaendtner J.

J Phys Chem B. 2016 Apr 28;120(16):3863-72. doi: 10.1021/acs.jpcb.6b01688. Epub 2016 Apr 19.

PMID:
27052057
35.

Folding and insertion thermodynamics of the transmembrane WALP peptide.

Bereau T, Bennett WF, Pfaendtner J, Deserno M, Karttunen M.

J Chem Phys. 2015 Dec 28;143(24):243127. doi: 10.1063/1.4935487.

PMID:
26723612
36.

New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations.

Fleming KL, Tiwary P, Pfaendtner J.

J Phys Chem A. 2016 Jan 21;120(2):299-305. doi: 10.1021/acs.jpca.5b10667. Epub 2016 Jan 7.

PMID:
26690335
37.

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics.

Pfaendtner J, Bonomi M.

J Chem Theory Comput. 2015 Nov 10;11(11):5062-7. doi: 10.1021/acs.jctc.5b00846. Epub 2015 Oct 9.

PMID:
26574304
38.

Structure Characterization and Properties of Metal-Surfactant Complexes Dispersed in Organic Solvents.

de la Iglesia P, Jaeger VW, Xi Y, Pfaendtner J, Pozzo LD.

Langmuir. 2015 Aug 25;31(33):9006-16. doi: 10.1021/acs.langmuir.5b02071. Epub 2015 Aug 10.

PMID:
26212253
39.

Trp-Cage Folding on Organic Surfaces.

Levine ZA, Fischer SA, Shea JE, Pfaendtner J.

J Phys Chem B. 2015 Aug 20;119(33):10417-25. doi: 10.1021/acs.jpcb.5b04213. Epub 2015 Aug 5.

PMID:
26207727
40.

Effect of Hydrophobic and Hydrophilic Surfaces on the Stability of Double-Stranded DNA.

Elder RM, Pfaendtner J, Jayaraman A.

Biomacromolecules. 2015 Jun 8;16(6):1862-9. doi: 10.1021/acs.biomac.5b00469. Epub 2015 May 21.

PMID:
25961882
41.

The general AMBER force field (GAFF) can accurately predict thermodynamic and transport properties of many ionic liquids.

Sprenger KG, Jaeger VW, Pfaendtner J.

J Phys Chem B. 2015 May 7;119(18):5882-95. doi: 10.1021/acs.jpcb.5b00689. Epub 2015 Apr 27.

PMID:
25853313
42.

Comparison of three ionic liquid-tolerant cellulases by molecular dynamics.

Jaeger V, Burney P, Pfaendtner J.

Biophys J. 2015 Feb 17;108(4):880-892. doi: 10.1016/j.bpj.2014.12.043.

43.

Molecular dynamics investigation of the ionic liquid/enzyme interface: application to engineering enzyme surface charge.

Burney PR, Nordwald EM, Hickman K, Kaar JL, Pfaendtner J.

Proteins. 2015 Apr;83(4):670-80. doi: 10.1002/prot.24757. Epub 2015 Feb 5.

PMID:
25641162
44.

Solvatochromism and conformational changes in fully dissolved poly(3-alkylthiophene)s.

Newbloom GM, Hoffmann SM, West AF, Gile MC, Sista P, Cheung HK, Luscombe CK, Pfaendtner J, Pozzo LD.

Langmuir. 2015 Jan 13;31(1):458-68. doi: 10.1021/la503666x. Epub 2014 Dec 22.

PMID:
25486225
45.

Tackling sampling challenges in biomolecular simulations.

Barducci A, Pfaendtner J, Bonomi M.

Methods Mol Biol. 2015;1215:151-71. doi: 10.1007/978-1-4939-1465-4_8.

PMID:
25330963
46.

Diatom mimics: directing the formation of biosilica nanoparticles by controlled folding of lysine-leucine peptides.

Baio JE, Zane A, Jaeger V, Roehrich AM, Lutz H, Pfaendtner J, Drobny GP, Weidner T.

J Am Chem Soc. 2014 Oct 29;136(43):15134-7. doi: 10.1021/ja5078238. Epub 2014 Oct 17.

47.

Fast Pyrolysis of Wood for Biofuels: Spatiotemporally Resolved Diffuse Reflectance In situ Spectroscopy of Particles.

Paulsen AD, Hough BR, Williams CL, Teixeira AR, Schwartz DT, Pfaendtner J, Dauenhauer PJ.

ChemSusChem. 2014 Feb 20. doi: 10.1002/cssc.201301056. [Epub ahead of print]

PMID:
24678023
48.

Ionic Liquids Can Selectively Change the Conformational Free-Energy Landscape of Sugar Rings.

Jarin Z, Pfaendtner J.

J Chem Theory Comput. 2014 Feb 11;10(2):507-10. doi: 10.1021/ct4010036. Epub 2014 Jan 24.

PMID:
26580028
49.

Structural effects of methionine oxidation on isolated subdomains of human fibrin D and αC regions.

Burney PR, White N, Pfaendtner J.

PLoS One. 2014 Jan 27;9(1):e86981. doi: 10.1371/journal.pone.0086981. eCollection 2014.

50.

Characterizing the catalyzed hydrolysis of β-1,4 glycosidic bonds using density functional theory.

Fleming KL, Pfaendtner J.

J Phys Chem A. 2013 Dec 27;117(51):14200-8. doi: 10.1021/jp4081178. Epub 2013 Dec 10.

PMID:
24266504

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