| The role of microRNA in the delayed negative feedback regulation of gene expression ZR Xie, HT Yang, WC Liu, MJ Hwang Biochemical and biophysical research communications 358 (3), 722-726, 2007 | 68 | 2007 |
| Methods for predicting protein–ligand binding sites ZR Xie, MJ Hwang Molecular modeling of proteins, 383-398, 2015 | 64 | 2015 |
| Has molecular docking ever brought us a medicine MA Phillips, MA Stewart, DL Woodling, ZR Xie Molecular docking 141, 2018 | 56 | 2018 |
| An interaction-motif-based scoring function for protein-ligand docking ZR Xie, MJ Hwang BMC bioinformatics 11, 1-16, 2010 | 49 | 2010 |
| A coarse-grained model for the simulations of biomolecular interactions in cellular environments ZR Xie, J Chen, Y Wu The Journal of Chemical Physics 140 (5), 2014 | 41 | 2014 |
| Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles ZR Xie, MJ Hwang Bioinformatics 28 (12), 1579-1585, 2012 | 40 | 2012 |
| A computational model for kinetic studies of cadherin binding and clustering J Chen, J Newhall, ZR Xie, D Leckband, Y Wu Biophysical Journal 111 (7), 1507-1518, 2016 | 34 | 2016 |
| Computational modeling of the interplay between cadherin-mediated cell adhesion and Wnt signaling pathway J Chen, ZR Xie, Y Wu PLoS One 9 (6), e100702, 2014 | 31 | 2014 |
| Predicting protein–protein association rates using coarse-grained simulation and machine learning ZR Xie, J Chen, Y Wu Scientific reports 7 (1), 46622, 2017 | 30 | 2017 |
| LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites ZR Xie, CK Liu, FC Hsiao, A Yao, MJ Hwang Nucleic acids research 41 (W1), W292-W296, 2013 | 27 | 2013 |
| Encapsulating Cas9 into extracellular vesicles by protein myristoylation JA Whitley, S Kim, L Lou, C Ye, OA Alsaidan, E Sulejmani, J Cai, ... Journal of extracellular vesicles 11 (4), e12196, 2022 | 25 | 2022 |
| Pharmacological inhibition of noncanonical EED-EZH2 signaling overcomes chemoresistance in prostate cancer X Li, L Gera, S Zhang, Y Chen, L Lou, LM Wilson, ZR Xie, G Sautto, D Liu, ... Theranostics 11 (14), 6873, 2021 | 23 | 2021 |
| Integrating structural information to study the dynamics of protein-protein interactions in cells B Wang, ZR Xie, J Chen, Y Wu Structure 26 (10), 1414-1424. e3, 2018 | 23 | 2018 |
| In silico identification of drug candidates against COVID-19 Y Wu, KY Chang, L Lou, LG Edwards, BK Doma, ZR Xie Informatics in Medicine Unlocked 21, 100461, 2020 | 22 | 2020 |
| Linking 3 D and 2 D binding kinetics of membrane proteins by multiscale simulations ZR Xie, J Chen, Y Wu Protein Science 23 (12), 1789-1799, 2014 | 22 | 2014 |
| Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method J Chen, ZR Xie, Y Wu Biomechanics and modeling in mechanobiology 15, 317-329, 2016 | 19 | 2016 |
| Engineering a PAM-flexible SpdCas9 variant as a universal gene repressor J Wang, Y Teng, R Zhang, Y Wu, L Lou, Y Zou, M Li, ZR Xie, Y Yan Nature communications 12 (1), 6916, 2021 | 18 | 2021 |
| A pilot study of all-computational drug design protocol–from structure prediction to interaction analysis Y Wu, L Lou, ZR Xie Frontiers in Chemistry 8, 81, 2020 | 13 | 2020 |
| Multiscale model for the assembly kinetics of protein complexes ZR Xie, J Chen, Y Wu The Journal of Physical Chemistry B 120 (4), 621-632, 2016 | 13 | 2016 |
| Decomposing the space of protein quaternary structures with the interface fragment pair library ZR Xie, J Chen, Y Zhao, Y Wu BMC bioinformatics 16, 1-10, 2015 | 13 | 2015 |
