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Deng, Nanjie
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1

Elucidating the Molecular Determinants of the Binding Modes..:

Sun, Qinfang ; Biswas, Avik ; Lyumkis, Dmitry..
Viruses.  16 (2024)  1 - p. 76 , 2024
Link: https://doi.org/10.3390/..
 
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2

Structure-based virtual screening workflow to identify anti..:

Sun, Qinfang ; Biswas, Avik ; Vijayan, R. S. K....
Journal of Computer-Aided Molecular Design.  36 (2022)  3 - p. 193-203 , 2022
Link: https://doi.org/10.1007/..
 
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3

Application of the alchemical transfer and potential of mea..:

Azimi, Solmaz ; Wu, Joe Z. ; Khuttan, Sheenam...
Journal of Computer-Aided Molecular Design.  36 (2022)  1 - p. 63-76 , 2022
Link: https://doi.org/10.1007/..
 
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4

Developing end-point methods for absolute binding free ener..:

Wickstrom, Lauren ; Gallicchio, Emilio ; Chen, Lieyang..
Physical Chemistry Chemical Physics.  24 (2022)  10 - p. 6037-6052 , 2022
Link: https://doi.org/10.1039/..
 
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5

Molecular Dynamics Free Energy Simulations Reveal the Mecha..:

Sun, Qinfang ; Levy, Ronald M. ; Kirby, Karen A....
Viruses.  13 (2021)  5 - p. 920 , 2021
Link: https://doi.org/10.3390/..
 
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6

Thermodynamic Decomposition of Solvation Free Energies with..:

Chen, Lieyang ; Cruz, Anthony ; Roe, Daniel R....
Journal of Chemical Theory and Computation.  17 (2021)  5 - p. 2714-2724 , 2021
Link: https://doi.org/10.1021/..
 
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7

Alchemical Transfer Approach to Absolute Binding Free Energ..:

Wu, Joe Z. ; Azimi, Solmaz ; Khuttan, Sheenam..
Journal of Chemical Theory and Computation.  17 (2021)  6 - p. 3309-3319 , 2021
Link: https://doi.org/10.1021/..
 
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8

Evaluating Molecular Docking Software for Small Molecule Bi..:

Dickerhoff, Jonathan ; Warnecke, Kassandra R. ; Wang, Kaibo..
International Journal of Molecular Sciences.  22 (2021)  19 - p. 10801 , 2021
Link: https://doi.org/10.3390/..
 
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9

Combining Alchemical Transformation with a Physical Pathway..:

Cruz, Jeffrey ; Wickstrom, Lauren ; Yang, Danzhou..
Journal of Chemical Theory and Computation.  16 (2020)  4 - p. 2803-2813 , 2020
Link: https://doi.org/10.1021/..
 
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10

Computational design of small molecular modulators of prote..:

Sun, Qinfang ; Ramaswamy, Vijayan S. K. ; Levy, Ronald.
Protein Science.  30 (2020)  2 - p. 438-447 , 2020
Link: https://doi.org/10.1002/..
 
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11

Absolute Protein Binding Free Energy Simulations for Ligand..:

Sakae, Yoshitake ; Zhang, Bin W. ; Levy, Ronald M..
Journal of Computational Chemistry.  41 (2019)  1 - p. 56-68 , 2019
Link: https://doi.org/10.1002/..
 
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12

Indenoisoquinoline Topoisomerase Inhibitors Strongly Bind a..:

Wang, Kai-Bo ; Elsayed, Mohamed S. A. ; Wu, Guanhui...
Journal of the American Chemical Society.  141 (2019)  28 - p. 11059-11070 , 2019
Link: https://doi.org/10.1021/..
 
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13

HIV-1 integrase tetramers are the antiviral target of pyrid..:

Koneru, Pratibha C ; Francis, Ashwanth C ; Deng, Nanjie...
eLife.  8 (2019)  - p. , 2019
Link: https://doi.org/10.7554/..
 
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14

Ligand Selectivity in the Recognition of Protoberberine Alk..:

Deng, Nanjie ; Xia, Junchao ; Wickstrom, Lauren...
Molecules.  24 (2019)  8 - p. 1574 , 2019
Link: https://doi.org/10.3390/..
 
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15

Comparing alchemical and physical pathway methods for compu..:

Deng, Nanjie ; Cui, Di ; Zhang, Bin W....
Physical Chemistry Chemical Physics.  20 (2018)  25 - p. 17081-17092 , 2018
Link: https://doi.org/10.1039/..
 
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