Research Output

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2020

Photopharmacological control of lipid function

Morstein, J. & Trauner, D., 2020, Methods in Enzymology. Chenoweth, D. M. (ed.). Academic Press Inc., p. 219-232 14 p. (Methods in Enzymology; vol. 638).

Research output: Chapter in Book/Report/Conference proceedingChapter

2018

Afterglow solid-state NMR spectroscopy

Abramov, G. & Traaseth, N. J., 2018, Methods in Molecular Biology. Humana Press Inc., p. 55-66 12 p. (Methods in Molecular Biology; vol. 1688).

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA nanotechnology: From the pub to information-based chemistry

Seeman, N. C., 2018, Methods in Molecular Biology. Humana Press Inc., p. 1-9 9 p. (Methods in Molecular Biology; vol. 1811).

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular mimetic self-assembly of anisotropic particles

Hueckel, T. & Sacanna, S., Jan 1 2018, Anisotropic Particle Assemblies: Synthesis, Assembly, Modeling, and Applications. Elsevier, p. 105-130 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

NMR spectroscopy approach to study the structure, orientation, and mechanism of the multidrug exporter EmrE

Leninger, M. & Traaseth, N. J., 2018, Methods in Molecular Biology. Humana Press Inc., p. 83-96 14 p. (Methods in Molecular Biology; vol. 1700).

Research output: Chapter in Book/Report/Conference proceedingChapter

2017

Designed 3D DNA crystals

Seeman, N. C., Sha, R., Birktoft, J., Zheng, J., Liu, W., Wang, T. & Mao, C., 2017, Methods in Molecular Biology. Humana Press Inc., p. 3-10 8 p. (Methods in Molecular Biology; vol. 1500).

Research output: Chapter in Book/Report/Conference proceedingChapter

Metal Complexes in Reverse Micelles

Walters, M. A., Nov 27 2017, Novel Nanoscale Hybrids. Wiley, p. 301-322 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

MFCC-Based Fragmentation Methods for Biomolecules

Liu, J., Zhu, T., He, X. & Zhang, J. Z. H., Jun 21 2017, Fragmentation: Toward Accurate Calculations on Complex Molecular Systems. Wiley, p. 323-348 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Modeling and design of peptidomimetics to modulate protein–protein interactions

Watkins, A. M., Bonneau, R. & Arora, P. S., 2017, Methods in Molecular Biology. Humana Press Inc., p. 291-307 17 p. (Methods in Molecular Biology; vol. 1561).

Research output: Chapter in Book/Report/Conference proceedingChapter

2016

Accurate Calculation of Electric Fields Inside Enzymes

Wang, X., He, X. & Zhang, J. Z. H., 2016, Computational Approaches for Studying Enzyme Mechanism Part B. Academic Press Inc., p. 45-72 28 p. (Methods in Enzymology; vol. 578).

Research output: Chapter in Book/Report/Conference proceedingChapter

Born–Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions

Zhou, Y., Wang, S., Li, Y. & Zhang, Y., 2016, Computational Approaches for Studying Enzyme Mechanism Part A. Voth, G. A. (ed.). Academic Press Inc., p. 105-118 14 p. (Methods in Enzymology; vol. 577).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chiroptical sensors

Canary, J. W., Duan, X. & Liu, X., Jan 1 2016, Encyclopedia of Spectroscopy and Spectrometry. Elsevier, p. 203-210 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Force field development with density-based energy decomposition analysis

Zhou, N., Wu, Q. & Zhang, Y., Mar 14 2016, Many-Body Effects and Electrostatics in Biomolecules. Pan Stanford Publishing Pte. Ltd., p. 121-145 25 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2015

Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: A hierarchical graph sampling approach

Kim, N., Zahran, M. & Schlick, T., 2015, Methods in Enzymology. Academic Press Inc., p. 115-135 21 p. (Methods in Enzymology; vol. 553).

Research output: Chapter in Book/Report/Conference proceedingChapter

Gibbs and Amistad

Kahr, B., Jan 1 2015, Culture of Chemistry: The Best Articles on the Human Side of 20th-Century Chemistry from the Archives of the Chemical Intelligencer. Hargittai, B. & Hargittai, I. (eds.). Springer US, p. 249-256 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular craftwork with DNA

Seeman, N. C., Jan 1 2015, Culture of Chemistry: The Best Articles on the Human Side of 20th-Century Chemistry from the Archives of the Chemical Intelligencer. Springer US, p. 141-152 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Supramolecular Polymers

Elacqua, E., Ten Brummelhuis, N. & Weck, M., Jan 1 2015, Volume 3: Polymer Synthesis. Wiley, Vol. 3-3. p. 71-92 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2014

1,3-Cyclohexadiene Formation Reactions: 6π and Higher-Order Electrocyclizations

Trauner, D. & Webster, R., Feb 2014, Comprehensive Organic Synthesis: Second Edition. Elsevier Ltd, Vol. 5. p. 783-826 44 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Chemical exchange saturation transfer contrast by glycosaminoglycans and its application for monitoring knee joint repair

Lee, J. S., Xia, D., Parasoglou, P., Chang, G., Jerschow, A. & Regatte, R. R., Jan 1 2014, Advanced Quantitative Imaging of Knee Joint Repair. World Scientific Publishing Co., p. 249-271 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Oxidation Adjacent to C X Bonds by Dehydrogenation

Stahl, S. S. & Diao, T., Feb 2014, Comprehensive Organic Synthesis: Second Edition. Elsevier Ltd, Vol. 7. p. 178-212 35 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polarizing Films

Kahr, B. & Knowles, K. M., Nov 24 2014, Iodine Chemistry and Applications. Wiley-Blackwell, Vol. 9781118466292. p. 479-488 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Time-dependent treatment of SVRT model for polyatom-polyatom reaction

Zhang, J. Z. H., 2014, Reaction Rate Constant Computations. Han, K. & Chu, T. (eds.). p. 337-351 15 p. (RSC Theoretical and Computational Chemistry Series).

Research output: Chapter in Book/Report/Conference proceedingChapter

2013

A 1H NMR Assay for measuring the photostationary states of photoswitchable ligands

Banghart, M. R. & Trauner, D., 2013, Chemical Neurobiology: Methods and Protocols. Banghart, M. (ed.). p. 107-120 14 p. (Methods in Molecular Biology; vol. 995).

Research output: Chapter in Book/Report/Conference proceedingChapter

An Orthosteric Inhibitor of the RAS-SOS Interaction

Nickerson, S., Joy, S. T., Arora, P. S. & Bar-Sagi, D., 2013, Enzymes. Academic Press, p. 25-39 15 p. (Enzymes; vol. 34).

Research output: Chapter in Book/Report/Conference proceedingChapter

Another important 60th anniversary

Seeman, N. C., 2013, Hierarchical Macromolecular Structures: 60 Years After The Staudinger Nobel Prize I. Springer New York LLC, p. 217-228 12 p. (Advances in Polymer Science; vol. 261).

Research output: Chapter in Book/Report/Conference proceedingChapter

Challenges and opportunities for optochemical genetics

Isacoff, E. Y., Kramer, R. H. & Trauner, D., Aug 28 2013, Optogenetics. Walter de Gruyter GmbH, p. 35-45 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Constrained peptide helices

Mahon, A. B. & Arora, P. S., Oct 1 2013, Understanding and Exploiting Protein-Protein Interactions as Drug Targets. Future Medicine Ltd., p. 63-73 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Graph applications to RNA structure and function

Kim, N., Fuhr, K. N. & Schlick, T., Jan 1 2013, Biophysics of RNA Folding. Springer New York, p. 23-51 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

SH3 Domains as Drug Targets

Luccarelli, J., Thompson, S. & Hamilton, A. D., Feb 26 2013, Protein-Protein Interactions in Drug Discovery. Wiley-VCH Verlag, Vol. 56. p. 101-128 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2012

2.19 Selected Diastereoselective Reactions: Electrocyclizations

Myers, E. L. & Trauner, D., Sep 2012, Comprehensive Chirality. Elsevier Ltd, Vol. 2. p. 563-606 44 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

8.30 Spectroscopic Analysis: Chiroptical Sensors

Canary, J. W., Dai, Z. & Mortezaei, S., Sep 2012, Comprehensive Chirality. Elsevier Ltd, Vol. 8. p. 600-624 25 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Ab Initio Molecular Dynamics Studies of Conjugated Dienes on Semiconductor Surfaces

Tuckerman, M. E. & Zhang, Y., Mar 20 2012, Functionalization of Semiconductor Surfaces. John Wiley and Sons, p. 233-276 44 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Chapter 4: Intrinsic motions of DNA polymerases underlie their remarkable specificity and selectivity and suggest a hybrid substrate binding mechanism

Foley, M. C., Arora, K. & Schlick, T., 2012, Innovations in Biomolecular Modeling and Simulations. Schlick, T. (ed.). p. 81-110 30 p. (RSC Biomolecular Sciences).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chiroptical Imaging of Crystals

Freudenthal, J., Kaminsky, W. & Kahr, B., Jan 31 2012, Comprehensive Chiroptical Spectroscopy. John Wiley and Sons, Vol. 1. p. 325-345 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Dynamic Stereochemistry and Chiroptical Spectroscopy of Metallo-Organic Compounds

Canary, J. W. & Dai, Z., Feb 17 2012, Comprehensive Chiroptical Spectroscopy. John Wiley and Sons, Vol. 2. p. 251-287 37 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Isotope labeling for solution and solid-state NMR spectroscopy of membrane proteins

Verardi, R., Traaseth, N. J., Masterson, L. R., Vostrikov, V. V. & Veglia, G., 2012, Isotope labeling in Biomolecular NMR. Atreya, H. S. (ed.). p. 35-62 28 p. (Advances in Experimental Medicine and Biology; vol. 992).

Research output: Chapter in Book/Report/Conference proceedingChapter

Pharmacology of bacterial and mycobacterial infections: Cell wall synthesis

Lupoli, T., Hooper, D. C., Arnaout, R. A., Kahne, D. & Walker, S., Oct 31 2012, Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy: Third Edition. Wolters Kluwer (UK) Ltd., p. 1280-1314 35 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Rational design strategies for developing synthetic inhibitors of helical protein interfaces

Mahon, A. B., Miller, S. E., Joy, S. T. & Arora, P. S., 2012, Protein-protein interactions. Wendt, MD. (ed.). Springer, p. 197-230 34 p. (Topics in Medicinal Chemistry; vol. 8).

Research output: Chapter in Book/Report/Conference proceedingChapter

The hybrid solution/solid-state NMR method for membrane protein structure determination

Veglia, G., Traaseth, N. J., Shi, L., Verardi, R., Gopinath, T. & Gustavsson, M., 2012, Comprehensive Biophysics. Elsevier Inc., Vol. 1. p. 182-198 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2011

Amino Acid-Based Dendrimers

Shi, Z., Zhou, C., Liu, Z., Totsingan, F. & Kallenbach, N. R., Apr 7 2011, Amino Acids, Peptides and Proteins in Organic Chemistry. Wiley-VCH, Vol. 4. p. 491-517 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Covalent polycyclic aromatic hydrocarbon-DNA adducts: Carcinogenicity, structure, and function

Broyde, S., Wang, L., Cai, Y., Jia, L., Shapiro, R., Patel, D. J. & Geacintov, N. E., 2011, Chemical Carcinogenesis. Penning, T. (ed.). p. 181-207 27 p. (Current Cancer Research; vol. 6).

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA polymerases structure, function, and modeling

Schlick, T., Jan 1 2011, Molecular Machines. World Scientific Publishing Co., p. 49-66 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Geranylgeranyltransferase-1 Inhibitors

Berndt, N., Hamilton, A. D. & Sebti, S. M., 2011, Enzymes. Academic Press, p. 129-163 35 p. (Enzymes; vol. 30).

Research output: Chapter in Book/Report/Conference proceedingChapter

Lectin microarrays: Simple tools for the analysis of complex glycans

Krishnamoorthy, L. & Mahal, L. K., 2011, Functional and Structural Proteomics of Glycoproteins. Springer Netherlands, p. 91-102 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Switchable Proteins and Channels

Volgraf, M., Banghart, M. & Trauner, D., Aug 29 2011, Molecular Switches, Second Edition. Wiley-VCH, Vol. 1. p. 563-593 31 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

The Exploration of Biomedical Multimodality in Small Solid Core Nanoparticles

Walters, M., Jul 18 2011, Hybrid Nanomaterials: Synthesis, Characterization, and Applications. John Wiley and Sons, p. 199-218 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2010

Elucidating Structure-Function Relationships in Bulky DNA Lesions: From Solution Structures to Polymerases

Broyde, S., Wang, L., Patel, D. J. & Geacintov, N. E., Oct 11 2010, The Chemical Biology of DNA Damage. Wiley-VCH, p. 331-352 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Functional imaging of the knee joint

Blumenkrantz, G., Li, X., Regatte, R. R., Jerschow, A. & Majumdar, S., Jan 1 2010, Advances in MRI of the Knee for Osteoarthritis. World Scientific Publishing Co., p. 185-233 49 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Inhibition of Protein-Protein Interactions by Peptide Mimics

Becerril, J., Rodriguez, J. M., Wyrembak, P. N. & Hamilton, A. D., Nov 30 2010, Protein Surface Recognition: Approaches for Drug Discovery. John Wiley and Sons, p. 105-131 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Introduction and Perspectives on the Chemistry and Biology of DNA Damage

Geacintov, N. E. & Broyde, S., Oct 11 2010, The Chemical Biology of DNA Damage. Wiley-VCH, p. 1-20 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter