Zhong-Ru (Paul) Xie - Publications

Institute of Biomedical Sciences Academia Sinica, Taipei, Taipei City, Taiwan 
 Institute of Biomedical Informatics National Yang-Ming University, Allendale Charter Township, Taipei City, Taiwan 
 2012-2013 Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego, La Jolla, CA 
 2013-2016 Department of Systems and Computational Biology Albert Einstein College of Medicine, New York, New York, United States 
 2016- College of Engineering University of Georgia, Athens, GA, United States 
Structural Bioinformatics, Computational Drug Discovery

27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Wang B, Xie ZR, Chen J, Wu Y. Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells. Structure (London, England : 1993). PMID 30174150 DOI: 10.1016/j.str.2018.07.010  1
2017 Xie ZR, Chen J, Wu Y. Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning. Scientific Reports. 7: 46622. PMID 28418043 DOI: 10.1038/srep46622  1
2016 Chen J, Xie ZR, Wu Y. Understand protein functions by comparing the similarity of local structural environments. Biochimica Et Biophysica Acta. PMID 27884635 DOI: 10.1016/j.bbapap.2016.11.008  1
2016 Chen J, Newhall J, Xie ZR, Leckband D, Wu Y. A Computational Model for Kinetic Studies of Cadherin Binding and Clustering. Biophysical Journal. 111: 1507-1518. PMID 27705773 DOI: 10.1016/j.bpj.2016.08.038  1
2016 Chen J, Xie ZR, Wu Y. Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27028148 DOI: 10.1089/cmb.2015.0227  1
2016 Xie ZR, Chen J, Wu Y. A Multi-Scale Model for the Assembling Kinetics of Protein Complexes. The Journal of Physical Chemistry. B. PMID 26738810 DOI: 10.1021/acs.jpcb.5b08962  0.92
2015 Chen J, Xie ZR, Wu Y. Elucidating the general principles of cell adhesion with a coarse-grained simulation model. Molecular Biosystems. PMID 26583681 DOI: 10.1039/c5mb00612k  1
2015 Chen J, Xie ZR, Wu Y. Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method. Biomechanics and Modeling in Mechanobiology. PMID 26049804 DOI: 10.1007/s10237-015-0690-0  0.92
2015 Xie ZR, Luo YL. Utility and cost-effectiveness of screening for hepatocellular carcinoma in a resource-limited setting. Medical Oncology (Northwood, London, England). 32: 88. PMID 25707770 DOI: 10.1007/s12032-015-0534-x  0.48
2015 Xie ZR, Chen J, Zhao Y, Wu Y. Decomposing the space of protein quaternary structures with the interface fragment pair library. Bmc Bioinformatics. 16: 14. PMID 25592649 DOI: 10.1186/s12859-014-0437-4  1
2015 Xie ZR, Hwang MJ. Methods for predicting protein-ligand binding sites. Methods in Molecular Biology (Clifton, N.J.). 1215: 383-98. PMID 25330972 DOI: 10.1007/978-1-4939-1465-4_17  1
2014 Xie ZR, Chen J, Wu Y. Linking 3D and 2D binding kinetics of membrane proteins by multiscale simulations. Protein Science : a Publication of the Protein Society. 23: 1789-99. PMID 25271078 DOI: 10.1002/pro.2574  1
2014 Chen J, Xie ZR, Wu Y. Computational modeling of the interplay between cadherin-mediated cell adhesion and Wnt signaling pathway. Plos One. 9: e100702. PMID 24967587 DOI: 10.1371/journal.pone.0100702  1
2014 Chen J, Xie ZR, Wu Y. A multiscale model for simulating binding kinetics of proteins with flexible linkers. Proteins. 82: 2512-22. PMID 24888574 DOI: 10.1002/prot.24614  1
2014 Xie ZR, Chen J, Wu Y. A coarse-grained model for the simulations of biomolecular interactions in cellular environments. The Journal of Chemical Physics. 140: 054112. PMID 24511927 DOI: 10.1063/1.4863992  1
2013 Sun WX, Wang HH, Jiang BC, Zhao YY, Xie ZR, Xiong K, Chen J. Global comparison of gene expression between subcutaneous and intramuscular adipose tissue of mature Erhualian pig. Genetics and Molecular Research : Gmr. 12: 5085-101. PMID 24301769 DOI: 10.4238/2013.October.29.3  1
2013 Xie ZR, Liu CK, Hsiao FC, Yao A, Hwang MJ. LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites. Nucleic Acids Research. 41: W292-6. PMID 23609546 DOI: 10.1093/nar/gkt300  1
2012 Xie ZR, Hwang MJ. Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles. Bioinformatics (Oxford, England). 28: 1579-85. PMID 22495747 DOI: 10.1093/bioinformatics/bts182  1
2012 Luo YL, Yang XL, Cui JB, Xiao FM, Liao Y, Wu T, Dong AH, Wan J, Xie ZR. Health-related quality of life of liver transplant recipients: a single center experience. Hepato-Gastroenterology. 59: 1947-50. PMID 22389272 DOI: 10.5754/hge12008  0.48
2011 Zhang YF, Xie ZR, Ni YQ, Mao R, Qi HZ, Yang YG, Jiang T, Bao YX. Curative effect of radiotherapy at various doses on subcutaneous alveolar echinococcosis in rats. Chinese Medical Journal. 124: 2845-8. PMID 22040490  0.48
2011 Bao YX, Mao R, Qi HZ, Zhang YF, Ni YQ, Xie ZR, Aziguli T, Wen H. [X-ray irradiation against Echinococcus multilocularis protoscoleces in vitro]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi = Chinese Journal of Parasitology & Parasitic Diseases. 29: 208-11. PMID 21970112  0.48
2011 Bao YX, Zhang YF, Ni YQ, Xie ZR, Qi HZ, Mao R, Yang YG, Wen H. [Effect of 6 MeV radiotherapy on secondary Echinococcus multilocularis infection in rats]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi = Chinese Journal of Parasitology & Parasitic Diseases. 29: 127-9. PMID 21826899  0.48
2010 Bao YX, Mao R, Xie ZR. [Radiotherapy in a case of osteohydatidosis]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi = Chinese Journal of Parasitology & Parasitic Diseases. 28: 1 p following 320. PMID 21140533  0.48
2010 Xie ZR, Hwang MJ. An interaction-motif-based scoring function for protein-ligand docking. Bmc Bioinformatics. 11: 298. PMID 20525216 DOI: 10.1186/1471-2105-11-298  1
2010 Zhang XJ, Wu JM, Xia CT, Zhu J, Xie ZR. [Extraction of rape seed proanthocyanidin with ultrasonic wave]. Zhong Yao Cai = Zhongyaocai = Journal of Chinese Medicinal Materials. 33: 114-8. PMID 20518317  0.48
2007 Xie ZR, Yang HT, Liu WC, Hwang MJ. The role of microRNA in the delayed negative feedback regulation of gene expression. Biochemical and Biophysical Research Communications. 358: 722-6. PMID 17509530 DOI: 10.1016/j.bbrc.2007.04.207  1
1985 Huang GQ, Xie ZR, Liu BL, Ning QZ, Shen PQ, Hong YK, Xi N, Li SH, Tan YS. [Evaluation of gastric juice lactic dehydrogenase (LDH) in the prognosis and recurrence of gastric cancer]. Sichuan Yi Xue Yuan Xue Bao = Acta Academiae Medicinae Sichuan. 16: 134-7. PMID 3016927  0.44
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