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Jeffrey R Wagner
Jeffrey R Wagner
Software Scientist, Open Force Field Initiative
Verified email at ucsd.edu - Homepage
Title
Cited by
Cited by
Year
Emerging computational methods for the rational discovery of allosteric drugs
JR Wagner, CT Lee, JD Durrant, RD Malmstrom, VA Feher, RE Amaro
Chemical reviews 116 (11), 6370-6390, 2016
2212016
POVME 3.0: software for mapping binding pocket flexibility
JR Wagner, J Sørensen, N Hensley, C Wong, C Zhu, T Perison, ...
Journal of chemical theory and computation 13 (9), 4584-4592, 2017
1942017
Development and benchmarking of open force field v1. 0.0—the parsley small-molecule force field
Y Qiu, DGA Smith, S Boothroyd, H Jang, DF Hahn, J Wagner, CC Bannan, ...
Journal of chemical theory and computation 17 (10), 6262-6280, 2021
1182021
Development and benchmarking of open force field 2.0. 0: the Sage small molecule force field
S Boothroyd, PK Behara, OC Madin, DF Hahn, H Jang, V Gapsys, ...
Journal of chemical theory and computation 19 (11), 3251-3275, 2023
482023
Continuous evaluation of ligand protein predictions: a weekly community challenge for drug docking
JR Wagner, CP Churas, S Liu, RV Swift, M Chiu, C Shao, VA Feher, ...
Structure 27 (8), 1326-1335. e4, 2019
432019
Stereoselective synthesis, biological evaluation, and modeling of novel bile acid-derived G-protein coupled bile acid receptor 1 (GP-BAR1, TGR5) agonists
DY Donna, KM Sousa, DL Mattern, J Wagner, X Fu, N Vaidehi, ...
Bioorganic & medicinal chemistry 23 (7), 1613-1628, 2015
392015
Quantum chemistry common driver and databases (QCDB) and quantum chemistry engine (QCEngine): Automation and interoperability among computational chemistry programs
DGA Smith, AT Lolinco, ZL Glick, J Lee, A Alenaizan, TA Barnes, ...
The Journal of chemical physics 155 (20), 2021
292021
Advanced techniques for constrained internal coordinate molecular dynamics
JR Wagner, GS Balaraman, MJM Niesen, AB Larsen, A Jain, N Vaidehi
Journal of computational chemistry 34 (11), 904-914, 2013
242013
Open force field BespokeFit: automating bespoke torsion parametrization at scale
JT Horton, S Boothroyd, J Wagner, JA Mitchell, T Gokey, DL Dotson, ...
Journal of chemical information and modeling 62 (22), 5622-5633, 2022
222022
Mapping conformational dynamics of proteins using torsional dynamics simulations
VK Gangupomu, JR Wagner, IH Park, A Jain, N Vaidehi
Biophysical journal 104 (9), 1999-2008, 2013
212013
Structure Refinement of Protein Low Resolution Models using GNEIMO Constrained Dynamics Method
IH Park, V Gangupomu, J Wagner, A Jain, N Vaidehi
Biophysical Journal 102 (3), 25a, 2012
212012
Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method
AB Larsen, JR Wagner, A Jain, N Vaidehi
Journal of Chemical Information and Modeling 54 (2), 508-517, 2014
152014
Determinants of oligonucleotide selectivity of APOBEC3B
JR Wagner, O Demir, MA Carpenter, H Aihara, DA Harki, RS Harris, ...
Journal of chemical information and modeling 59 (5), 2264-2273, 2018
142018
GneimoSim: A modular internal coordinates molecular dynamics simulation package
AB Larsen, JR Wagner, S Kandel, R Salomon‐Ferrer, N Vaidehi, A Jain
Journal of computational chemistry 35 (31), 2245-2255, 2014
92014
Collaborative assessment of molecular geometries and energies from the Open Force Field
L D’Amore, DF Hahn, DL Dotson, JT Horton, J Anwar, I Craig, T Fox, ...
Journal of chemical information and modeling 62 (23), 6094-6104, 2022
82022
Fixman compensating potential for general branched molecules
A Jain, S Kandel, J Wagner, A Larsen, N Vaidehi
The Journal of Chemical Physics 139 (24), 2013
82013
hyejang,; Rodrıguez-Guerra, J. openforcefield/openforcefields: Version 1.2. 1” Parsley” Update
J Wagner, M Thompson, D Dotson
7
openforce-field/openforcefields: Version 1.0. 0 “Parsley”
Y Qiu, DGA Smith, S Boothroyd, J Wagner, CC Bannan, T Gokey, H Jang, ...
Zenodo, 2019
42019
Development and benchmarking of an open, self-consistent force field for proteins and small molecules from the open force field initiative
CE Cavender, PK Behara, S Boothroyd, DL Dotson, JT Horton, JA Mitchell, ...
Biophysical Journal 122 (3), 421a, 2023
12023
Determinants of Substrate Specificity in APOBEC3B
J Wagner, Ö Demir, MA Carpenter, H Aihara, DA Harki, RS Harris, ...
12018
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Articles 1–20