AmberTools users’ manual

Thomas J Macke , W Svrcek-Seiler , Russell A Brown , István Kolossváry
Smpte Journal

31
2010
A GPU based Conformational Entropy Calculation Method

Junmei Wang , José M. García , Horacio Emilio Pérez Sánchez , Qian Zhang
IWBBIO 735 -743

1
2013
A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

Junmei Wang , Ray Luo , D Artagnan Greene , Li Xiao
arXiv: Biological Physics

22
2017
Determination of van der Waals Parameters Using a Double Exponential Potential for Nonbonded Divalent Metal Cations in TIP3P Solvent.

Viet Hoang Man , Xiongwu Wu , Xibing He , Xiang-Qun Xie
Journal of Chemical Theory and Computation 17 ( 2) 1086 -1097

9
2021
Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities.

Junmei Wang , Viet Hoang Man , Xibing He , Beihong Ji
Journal of Cheminformatics 13 ( 1) 11

2021
Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction.

Junmei Wang , Viet Hoang Man , Xibing He , Beihong Ji
Briefings in Bioinformatics

1
2021
Drug-Drug Interaction Between Oxycodone and Diazepam by a Combined in Silico Pharmacokinetic and Pharmacodynamic Modeling Approach.

Beihong Ji , Ying Xue , Yuanyuan Xu , Shuhan Liu
ACS Chemical Neuroscience 12 ( 10) 1777 -1790

2021
VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations.

Huiyong Sun , Junmei Wang , Tingjun Hou , Hui Liu
Journal of Chemical Information and Modeling

10
2021
In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor.

Junmei Wang , Viet Hoang Man , Xibing He , Beihong Ji
Briefings in Bioinformatics

2021
How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules

Junmei Wang , Piotr Cieplak , Peter A. Kollman
Journal of Computational Chemistry 21 ( 12) 1049 -1074

3,026
2000
Advances in Computationally Modeling Human Oral Bioavailability

Junmei Wang , Tingjun Hou
Advanced Drug Delivery Reviews 86 11 -16

20
2015
The application of in silico drug-likeness predictions in pharmaceutical research

Sheng Tian , Junmei Wang , Youyong Li , Dan Li
Advanced Drug Delivery Reviews 86 2 -10

307
2015
Recent advances in computational prediction of drug absorption and permeability in drug discovery.

Tingjun Hou , Junmei Wang , Wei Zhang , Wei Wang
Current Medicinal Chemistry 13 ( 22) 2653 -2667

174
2006
Crystal structure of the human NK1 tachykinin receptor.

Jie Yin , Karen Chapman , Lindsay D. Clark , Zhenhua Shao
Proceedings of the National Academy of Sciences of the United States of America 115 ( 52) 13264 -13269

13
2018
Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

Jun Shang , Ben Hu , Junmei Wang , Feng Zhu
Journal of Chemical Information and Modeling 58 ( 6) 1182 -1193

21
2018
Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator

Na Liu , Wenfang Zhou , Yue Guo , Junmei Wang
Journal of Chemical Information and Modeling 58 ( 8) 1652 -1661

31
2018
Dihydrostreptomycin Directly Binds to, Modulates, and Passes through the MscL Channel Pore

Irene Iscla , Ya Gao , Hua Li , Junmei Wang
PLOS Biology 14 ( 6) e1002473

17
2016
Structural Basis of TLR2/TLR1 Activation by the Synthetic Agonist Diprovocim

Lijing Su , Ying Wang , Junmei Wang , Yuto Mifune
Journal of Medicinal Chemistry 62 ( 6) 2938 -2949

4
2019
Recent advances in free energy calculations with a combination of molecular mechanics and continuum models

Junmei Wang , Tingjun Hou , Xiaojie Xu
Current Computer - Aided Drug Design 2 ( 3) 287 -306

218
2006
How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?

Dongxiao Hao , Xibing He , Beihong Ji , Shengli Zhang
Journal of Chemical Information and Modeling 60 ( 12) 6624 -6633

2020