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Niel M Henriksen
Niel M Henriksen
UCSD, Atomwise
Verified email at ucsd.edu
Title
Cited by
Cited by
Year
Overview of the SAMPL5 host–guest challenge: Are we doing better?
J Yin, NM Henriksen, DR Slochower, MR Shirts, MW Chiu, DL Mobley, ...
Journal of computer-aided molecular design 31, 1-19, 2017
1862017
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields
C Bergonzo, NM Henriksen, DR Roe, TE Cheatham
Rna 21 (9), 1578-1590, 2015
1472015
Multidimensional replica exchange molecular dynamics yields a converged ensemble of an RNA tetranucleotide
C Bergonzo, NM Henriksen, DR Roe, JM Swails, AE Roitberg, ...
Journal of Chemical Theory and Computation 10 (1), 492-499, 2014
1422014
Computational calorimetry: high-precision calculation of host–guest binding thermodynamics
NM Henriksen, AT Fenley, MK Gilson
Journal of chemical theory and computation 11 (9), 4377-4394, 2015
1232015
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations
A Rizzi, T Jensen, DR Slochower, M Aldeghi, V Gapsys, D Ntekoumes, ...
Journal of computer-aided molecular design 34 (5), 601-633, 2020
1092020
Bridging calorimetry and simulation through precise calculations of cucurbituril–guest binding enthalpies
AT Fenley, NM Henriksen, HS Muddana, MK Gilson
Journal of chemical theory and computation 10 (9), 4069-4078, 2014
1062014
Hydrophobe challenge: A joint experimental and computational study on the host–guest binding of hydrocarbons to cucurbiturils, allowing explicit evaluation of guest hydration …
KI Assaf, M Florea, J Antony, NM Henriksen, J Yin, A Hansen, Z Qu, ...
The Journal of Physical Chemistry B 121 (49), 11144-11162, 2017
822017
Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations
NM Henriksen, DR Roe, TE Cheatham III
The journal of physical chemistry B 117 (15), 4014-4027, 2013
702013
Antitumor activity of 1, 18-octadecanedioic acid-paclitaxel complexed with human serum albumin
CE Callmann, CLM LeGuyader, ST Burton, MP Thompson, R Hennis, ...
Journal of the American Chemical Society 141 (30), 11765-11769, 2019
682019
Evaluation and minimization of uncertainty in ITC binding measurements: heat error, concentration error, saturation, and stoichiometry
SA Kantonen, NM Henriksen, MK Gilson
Biochimica et Biophysica Acta (BBA)-General Subjects 1861 (2), 485-498, 2017
672017
Evaluating force field performance in thermodynamic calculations of cyclodextrin host–guest binding: Water models, partial charges, and host force field parameters
NM Henriksen, MK Gilson
Journal of chemical theory and computation 13 (9), 4253-4269, 2017
662017
Attach-pull-release calculations of ligand binding and conformational changes on the first BRD4 bromodomain
G Heinzelmann, NM Henriksen, MK Gilson
Journal of chemical theory and computation 13 (7), 3260-3275, 2017
642017
Araiosamines A−D: Tris-bromoindole Cyclic Guanidine Alkaloids from the Marine Sponge Clathria (Thalysias) araiosa
X Wei, NM Henriksen, JJ Skalicky, MK Harper, TE Cheatham III, ...
The Journal of organic chemistry 76 (14), 5515-5523, 2011
502011
The SAMPL5 host–guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method
J Yin, NM Henriksen, DR Slochower, MK Gilson
Journal of computer-aided molecular design 31, 133-145, 2017
432017
Totopotensamides, Polyketide–Cyclic Peptide Hybrids from a Mollusk-Associated Bacterium Streptomyces sp.
Z Lin, M Flores, I Forteza, NM Henriksen, GP Concepcion, G Rosenberg, ...
Journal of natural products 75 (4), 644-649, 2012
432012
Toward improved force-field accuracy through sensitivity analysis of host-guest binding thermodynamics
J Yin, AT Fenley, NM Henriksen, MK Gilson
The Journal of Physical Chemistry B 119 (32), 10145-10155, 2015
422015
Binding enthalpy calculations for a neutral host–guest pair yield widely divergent salt effects across water models
K Gao, J Yin, NM Henriksen, AT Fenley, MK Gilson
Journal of chemical theory and computation 11 (10), 4555-4564, 2015
402015
Binding thermodynamics of Host–Guest Systems with SMIRNOFF99Frosst 1.0. 5 from the open force field initiative
DR Slochower, NM Henriksen, LP Wang, JD Chodera, DL Mobley, ...
Journal of chemical theory and computation 15 (11), 6225-6242, 2019
362019
Bind3p: optimization of a water model based on host–guest binding data
J Yin, NM Henriksen, HS Muddana, MK Gilson
Journal of chemical theory and computation 14 (7), 3621-3632, 2018
332018
Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure
NM Henriksen, DR Davis, TE Cheatham III
Journal of biomolecular NMR 53, 321-339, 2012
322012
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