| 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 | 249 | 2016 |
| 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 | 219 | 2017 |
| 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 | 151 | 2021 |
| 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 | 107 | 2023 |
| 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 | 46 | 2019 |
| 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 | 43 | 2021 |
| 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 | 40 | 2015 |
| 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 | 37 | 2022 |
| 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 | 25 | 2013 |
| 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 | 22 | 2013 |
| 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 | 21 | 2012 |
| 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 | 18 | 2022 |
| 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 | 17 | 2018 |
| 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 | 15 | 2014 |
| 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 | 9 | 2014 |
| 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 | 8 | 2013 |
| openforce-field/openforcefields: Version 1.0. 0 “Parsley” Y Qiu, DGA Smith, S Boothroyd, J Wagner, CC Bannan, T Gokey, H Jang, ... Zenodo, 2019 | 7 | 2019 |
| hyejang,; Rodrıguez-Guerra, J. openforcefield/openforcefields: Version 1.2. 1” Parsley” Update J Wagner, M Thompson, D Dotson | 7 | |
| 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 | 2 | 2023 |
| Determinants of Substrate Specificity in APOBEC3B J Wagner, Ö Demir, MA Carpenter, H Aihara, DA Harki, RS Harris, ... | 1 | 2018 |
