Dr. Zhong-Ru Xie, PhD - University of Georgia - Assistant Professor

Dr. Zhong-Ru Xie

PhD

University of Georgia

Assistant Professor

Athens, GA | United States

Main Specialties: Biology

Additional Specialties: Computational & Systems Biology


Top Author

Dr. Zhong-Ru Xie, PhD - University of Georgia - Assistant Professor

Dr. Zhong-Ru Xie

PhD

Introduction

Primary Affiliation: University of Georgia - Athens, GA , United States

Specialties:

Additional Specialties:


View Dr. Zhong-Ru Xie’s Resume / CV

Education

Jan 2011
Institute of Biomedical Informatics
Ph. D

Experience

Aug 2016
College of Engineering, University of Georgia
Assistant Professor

Publications

17Publications

103Reads

444Profile Views

69PubMed Central Citations

Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells.

Structure 2018 Oct 30;26(10):1414-1424.e3. Epub 2018 Aug 30.

Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2018.07.010DOI Listing
October 2018
12 Reads
5.620 Impact Factor

Understand protein functions by comparing the similarity of local structural environments.

Biochim Biophys Acta Proteins Proteom 2017 Feb 22;1865(2):142-152. Epub 2016 Nov 22.

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, United States. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2016.11.008DOI Listing
February 2017
5 Reads
2.750 Impact Factor

A Computational Model for Kinetic Studies of Cadherin Binding and Clustering.

Biophys J 2016 Oct;111(7):1507-1518

Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2016.08.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052510PMC
October 2016
7 Reads
1 Citation
3.972 Impact Factor

Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method.

J Comput Biol 2016 07 30;23(7):566-84. Epub 2016 Mar 30.

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University , Bronx, New York.

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http://dx.doi.org/10.1089/cmb.2015.0227DOI Listing
July 2016
5 Reads
1.740 Impact Factor

Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method.

Biomech Model Mechanobiol 2016 Apr 7;15(2):317-29. Epub 2015 Jun 7.

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.

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http://dx.doi.org/10.1007/s10237-015-0690-0DOI Listing
April 2016
6 Reads
3 Citations

Multiscale Model for the Assembly Kinetics of Protein Complexes.

J Phys Chem B 2016 Feb 20;120(4):621-32. Epub 2016 Jan 20.

Department of Systems and Computational Biology, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.

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http://dx.doi.org/10.1021/acs.jpcb.5b08962DOI Listing
February 2016
5 Reads
5 Citations

Elucidating the general principles of cell adhesion with a coarse-grained simulation model.

Mol Biosyst 2016 Jan 19;12(1):205-18. Epub 2015 Nov 19.

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

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http://dx.doi.org/10.1039/c5mb00612kDOI Listing
January 2016
5 Reads
1 Citation

Methods for predicting protein-ligand binding sites.

Methods Mol Biol 2015 ;1215:383-98

Institute of Biomedical Sciences, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 115, Taiwan.

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http://dx.doi.org/10.1007/978-1-4939-1465-4_17DOI Listing
June 2015
6 Reads
4 Citations

Computational modeling of the interplay between cadherin-mediated cell adhesion and Wnt signaling pathway.

PLoS One 2014 26;9(6):e100702. Epub 2014 Jun 26.

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100702PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072676PMC
February 2015
5 Reads
3 Citations
3.234 Impact Factor

Decomposing the space of protein quaternary structures with the interface fragment pair library.

BMC Bioinformatics 2015 Jan 16;16:14. Epub 2015 Jan 16.

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.

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http://dx.doi.org/10.1186/s12859-014-0437-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384354PMC
January 2015
6 Reads
1 Citation
2.580 Impact Factor

Linking 3D and 2D binding kinetics of membrane proteins by multiscale simulations.

Protein Sci 2014 Dec 21;23(12):1789-99. Epub 2014 Oct 21.

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, 10461.

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http://dx.doi.org/10.1002/pro.2574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253819PMC
December 2014
5 Reads
3 Citations
2.854 Impact Factor

A multiscale model for simulating binding kinetics of proteins with flexible linkers.

Proteins 2014 Oct 9;82(10):2512-22. Epub 2014 Jun 9.

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, 10461.

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http://dx.doi.org/10.1002/prot.24614DOI Listing
October 2014
8 Reads
4 Citations
2.630 Impact Factor

A coarse-grained model for the simulations of biomolecular interactions in cellular environments.

J Chem Phys 2014 Feb;140(5):054112

Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, USA.

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http://dx.doi.org/10.1063/1.4863992DOI Listing
February 2014
5 Reads
5 Citations
2.952 Impact Factor

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites.

Nucleic Acids Res 2013 Jul 22;41(Web Server issue):W292-6. Epub 2013 Apr 22.

Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.

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http://dx.doi.org/10.1093/nar/gkt300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692107PMC
July 2013
6 Reads
4 Citations
9.112 Impact Factor

Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles.

Bioinformatics 2012 Jun 11;28(12):1579-85. Epub 2012 Apr 11.

Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan.

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http://dx.doi.org/10.1093/bioinformatics/bts182DOI Listing
June 2012
4 Reads
9 Citations
4.981 Impact Factor

An interaction-motif-based scoring function for protein-ligand docking.

BMC Bioinformatics 2010 Jun 2;11:298. Epub 2010 Jun 2.

Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.

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http://dx.doi.org/10.1186/1471-2105-11-298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098071PMC
June 2010
7 Reads
10 Citations
2.580 Impact Factor

The role of microRNA in the delayed negative feedback regulation of gene expression.

Biochem Biophys Res Commun 2007 Jul 11;358(3):722-6. Epub 2007 May 11.

Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan.

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http://dx.doi.org/10.1016/j.bbrc.2007.04.207DOI Listing
July 2007
6 Reads
16 Citations
2.300 Impact Factor