Niel Henriksen

TitlePostdoctoral Scholar
InstitutionUniversity of California San Diego
DepartmentSchool of Pharmacy and Pharmaceutical Science
Address9500 Gilman Drive #0719
La Jolla CA 92093
vCardDownload vCard

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Yin J, Henriksen N, Muddana HS, Gilson MK. Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data. J Chem Theory Comput. 2018 Jun 06. PMID: 29874074.
      View in: PubMed
    2. Hayatshahi HS, Henriksen N, Cheatham TE. Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations. J Chem Theory Comput. 2018 Mar 13; 14(3):1456-1470. PMID: 29323894.
      View in: PubMed
    3. Kantonen SA, Henriksen N, Gilson MK. Accounting for apparent deviations between calorimetric and van't Hoff enthalpies. Biochim Biophys Acta. 2018 03; 1862(3):692-704. PMID: 29221984.
      View in: PubMed
    4. Assaf KI, Florea M, Antony J, Henriksen N, Yin J, Hansen A, Qu ZW, Sure R, Klapstein D, Gilson MK, Grimme S, Nau WM. HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions. J Phys Chem B. 2017 12 14; 121(49):11144-11162. PMID: 29140701.
      View in: PubMed
    5. Henriksen N, Gilson MK. Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. J Chem Theory Comput. 2017 Sep 12; 13(9):4253-4269. PMID: 28696692.
      View in: PubMed
    6. Heinzelmann G, Henriksen N, Gilson MK. Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain. J Chem Theory Comput. 2017 Jul 11; 13(7):3260-3275. PMID: 28564537.
      View in: PubMed
    7. Lee KS, Henriksen N, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD. Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase. Arch Biochem Biophys. 2017 Jan 01; 613:1-11. PMID: 27983948.
      View in: PubMed
    8. Yin J, Henriksen N, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Overview of the SAMPL5 host-guest challenge: Are we doing better? J Comput Aided Mol Des. 2017 Jan; 31(1):1-19. PMID: 27658802.
      View in: PubMed
    9. Yin J, Henriksen N, Slochower DR, Gilson MK. The SAMPL5 host-guest challenge: computing binding free energies andĀ enthalpies from explicit solvent simulations by the attach-pull-release (APR) method. J Comput Aided Mol Des. 2017 Jan; 31(1):133-145. PMID: 27638809.
      View in: PubMed
    10. Kantonen SA, Henriksen N, Gilson MK. Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry. Biochim Biophys Acta. 2017 02; 1861(2):485-498. PMID: 27599357.
      View in: PubMed
    11. Gao K, Yin J, Henriksen N, Fenley AT, Gilson MK. Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models. J Chem Theory Comput. 2015 Oct 13; 11(10):4555-64. PMID: 26574247; PMCID: PMC4668924 [Available on 10/13/16].
    12. Henriksen N, Fenley AT, Gilson MK. Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics. J Chem Theory Comput. 2015 Sep 08; 11(9):4377-94. PMID: 26523125; PMCID: PMC4614838.
    13. Yin J, Fenley AT, Henriksen N, Gilson MK. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics. J Phys Chem B. 2015 Aug 13; 119(32):10145-55. PMID: 26181208; PMCID: PMC4664157.
    14. Bergonzo C, Henriksen N, Roe DR, Cheatham TE. Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields. RNA. 2015 Sep; 21(9):1578-90. PMID: 26124199; PMCID: PMC4536319.
    15. Fenley AT, Henriksen N, Muddana HS, Gilson MK. Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies. J Chem Theory Comput. 2014 Sep 09; 10(9):4069-4078. PMID: 25221445.
      View in: PubMed
    16. Henriksen N, Hayatshahi HS, Davis DR, Cheatham TE. Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations. J Chem Inf Model. 2014 Jun 23; 54(6):1758-72. PMID: 24835734; PMCID: PMC4076022.
    17. Bergonzo C, Henriksen N, Roe DR, Swails JM, Roitberg AE, Cheatham TE. Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide. J Chem Theory Comput. 2014 Jan 14; 10(1):492-499. PMID: 24453949.
      View in: PubMed
    18. Henriksen N, Roe DR, Cheatham TE. Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations. J Phys Chem B. 2013 Apr 18; 117(15):4014-27. PMID: 23477537; PMCID: PMC3775460.
    19. Henriksen N, Davis DR, Cheatham TE. Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure. J Biomol NMR. 2012 Aug; 53(4):321-39. PMID: 22714631; PMCID: PMC3405240.
    20. Lin Z, Flores M, Forteza I, Henriksen N, Concepcion GP, Rosenberg G, Haygood MG, Olivera BM, Light AR, Cheatham TE, Schmidt EW. Totopotensamides, polyketide-cyclic peptide hybrids from a mollusk-associated bacterium Streptomyces sp. J Nat Prod. 2012 Apr 27; 75(4):644-9. PMID: 22439622; PMCID: PMC3338888.
    21. Wei X, Henriksen N, Skalicky JJ, Harper MK, Cheatham TE, Ireland CM, Van Wagoner RM. Araiosamines A-D: tris-bromoindole cyclic guanidine alkaloids from the marine sponge Clathria (Thalysias) araiosa. J Org Chem. 2011 Jul 15; 76(14):5515-23. PMID: 21462976; PMCID: PMC3188435.