Xiaoqin Zou

Xiaoqin Zou

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Xiaoqin Zou

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Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment.

Authors:
Marc F Lensink Guillaume Brysbaert Nurul Nadzirin Sameer Velankar Raphaël A G Chaleil Tereza Gerguri Paul A Bates Elodie Laine Alessandra Carbone Sergei Grudinin Ren Kong Ran-Ran Liu Xi-Ming Xu Hang Shi Shan Chang Miriam Eisenstein Agnieszka Karczynska Cezary Czaplewski Emilia Lubecka Agnieszka Lipska Paweł Krupa Magdalena Mozolewska Łukasz Golon Sergey Samsonov Adam Liwo Silvia Crivelli Guillaume Pagès Mikhail Karasikov Maria Kadukova Yumeng Yan Sheng-You Huang Mireia Rosell Luis Angel Rodríguez-Lumbreras Miguel Romero-Durana Lucía Díaz-Bueno Juan Fernandez-Recio Charles Christoffer Genki Terashi Woong-Hee Shin Tunde Aderinwale Sai Raghavendra Maddhuri Venkata Subraman Daisuke Kihara Dima Kozakov Sandor Vajda Kathyn Porter Dzmitry Padhorny Israel Desta Dmitri Beglov Mikhail Ignatov Sergey Kotelnikov Iain H Moal David W Ritchie Isaure Chauvot de Beauchêne Bernard Maigret Marie-Dominique Devignes Maria Elisa Ruiz Echartea Didier Barradas-Bautista Zhen Cao Luigi Cavallo Romina Oliva Yue Cao Yang Shen Minkyung Baek Taeyong Park Hyeonuk Woo Chaok Seok Merav Braitbard Lirane Bitton Dina Scheidman-Duhovny Justas DapkŪnas Kliment Olechnovič Česlovas Venclovas Petras J Kundrotas Saveliy Belkin Devlina Chakravarty Varsha D Badal Ilya A Vakser Thom Vreven Sweta Vangaveti Tyler Borrman Zhiping Weng Johnathan D Guest Ragul Gowthaman Brian G Pierce Xianjin Xu Rui Duan Liming Qiu Jie Hou Benjamin Ryan Merideth Zhiwei Ma Jianlin Cheng Xiaoqin Zou Panos I Koukos Jorge Roel-Touris Francesco Ambrosetti Cunliang Geng Jörg Schaarschmidt Mikael E Trellet Adrien S J Melquiond Li Xue Brian Jiménez-García Charlotte W van Noort Rodrigo V Honorato Alexandre M J J Bonvin Shoshana J Wodak

Proteins 2019 Oct 14. Epub 2019 Oct 14.

VIB Structural Biology Research Center, VUB, Pleinlaan 2, B-1050, Brussels, Belgium.

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http://dx.doi.org/10.1002/prot.25838DOI Listing
October 2019

Identifying the molecular target sites for CFTR potentiators GLPG1837 and VX-770.

J Gen Physiol 2019 Jul 4;151(7):912-928. Epub 2019 Jun 4.

Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO

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http://dx.doi.org/10.1085/jgp.201912360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6605684PMC
July 2019

Small-pore CAU-21 and porous PIM-1 in mixed-matrix membranes for improving selectivity and permeability in hydrogen separation.

Chem Commun (Camb) 2019 Jun;55(49):7101-7104

Faculty of Chemistry, Northeast Normal University, Changchun 130024, China.

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http://dx.doi.org/10.1039/c9cc02537eDOI Listing
June 2019

Constructing Connected Paths between UiO-66 and PIM-1 to Improve Membrane CO Separation with Crystal-Like Gas Selectivity.

Adv Mater 2019 Apr 25;31(15):e1806853. Epub 2019 Feb 25.

Faculty of Chemistry, Northeast Normal University, Changchun, 130024, P. R. China.

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http://dx.doi.org/10.1002/adma.201806853DOI Listing
April 2019

Stathmin gene silencing suppresses proliferation, migration and invasion of gastric cancer cells via AKT/sCLU and STAT3 signaling.

Int J Oncol 2019 Mar 3;54(3):1086-1098. Epub 2019 Jan 3.

Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China.

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http://dx.doi.org/10.3892/ijo.2019.4674DOI Listing
March 2019

Predicting protein-ligand binding modes for CELPP and GC3: workflows and insight.

J Comput Aided Mol Des 2019 Mar 28;33(3):367-374. Epub 2019 Jan 28.

Dalton Cardiovascular Research Center, University of Missouri, 65211, Columbia, MO, USA.

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http://dx.doi.org/10.1007/s10822-019-00185-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6494980PMC
March 2019

A Crystalline Polyimide Porous Organic Framework for Selective Adsorption of Acetylene over Ethylene.

J Am Chem Soc 2018 11 6;140(46):15724-15730. Epub 2018 Nov 6.

State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry , Jilin University , Changchun 130012 , China.

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http://dx.doi.org/10.1021/jacs.8b08174DOI Listing
November 2018

MDockPeP: An ab-initio protein-peptide docking server.

J Comput Chem 2018 10 23;39(28):2409-2413. Epub 2018 Oct 23.

Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Informatics Institute, University of Missouri, Columbia, Missouri, 65211.

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http://doi.wiley.com/10.1002/jcc.25555
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http://dx.doi.org/10.1002/jcc.25555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226323PMC
October 2018

Molecularly Imprinted Porous Aromatic Frameworks Serving as Porous Artificial Enzymes.

Adv Mater 2018 Jul 21;30(27):e1800069. Epub 2018 May 21.

Key Laboratory of Polyoxometalate Science of Ministry of Education, Northeast Normal University, Renmin Avenue, Changchun, 130024, China.

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http://dx.doi.org/10.1002/adma.201800069DOI Listing
July 2018

Hard-template synthesis of micro-mesoporous organic frameworks with controlled hierarchicity.

Chem Commun (Camb) 2018 Jul;54(60):8335-8338

State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China.

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http://dx.doi.org/10.1039/c8cc04029jDOI Listing
July 2018

Effects of Kudingcha Nanoparticles in Hyperlipidaemic Rats Induced by a High Fat Diet.

Cell Physiol Biochem 2018 10;45(6):2257-2267. Epub 2018 Mar 10.

The department of pharmacy, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.

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http://dx.doi.org/10.1159/000488171DOI Listing
June 2018

A zeolite-like aluminophosphate membrane with molecular-sieving property for water desalination.

Chem Sci 2018 Mar 24;9(9):2533-2539. Epub 2018 Jan 24.

Faculty of Chemistry , Northeast Normal University , Changchun 130024 , P. R. China.

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http://dx.doi.org/10.1039/c7sc04974aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909670PMC
March 2018

The Usage of ACCLUSTER for Peptide Binding Site Prediction.

Methods Mol Biol 2017 ;1561:3-9

Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, Informatics Institute, University of Missouri, 134 Research Park Drive, 117A Dalton Bldg, Columbia, MO, 65211, USA.

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http://dx.doi.org/10.1007/978-1-4939-6798-8_1DOI Listing
February 2018

Docking-based inverse virtual screening: methods, applications, and challenges.

Biophys Rep 2018 1;4(1):1-16. Epub 2018 Feb 1.

1Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 USA.

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http://dx.doi.org/10.1007/s41048-017-0045-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860130PMC
February 2018

Microporous Organic Materials for Membrane-Based Gas Separation.

Adv Mater 2018 Jan 24;30(3). Epub 2017 Oct 24.

Faculty of Chemistry, Northeast Normal University, Changchun, 130024, P. R. China.

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http://dx.doi.org/10.1002/adma.201700750DOI Listing
January 2018

Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor.

J Comput Aided Mol Des 2018 01 10;32(1):103-111. Epub 2017 Nov 10.

Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.

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http://dx.doi.org/10.1007/s10822-017-0082-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767536PMC
January 2018

Modeling of flux, binding and substitution of urea molecules in the urea transporter dvUT.

J Mol Graph Model 2017 09 25;76:504-511. Epub 2017 Apr 25.

Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry and Informatics Institute, University of Missouri, Columbia, MO 65211, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jmgm.2017.04.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5685562PMC
September 2017

Porous Aromatic Frameworks for Size-Selective Halogenation of Aryl Compounds.

ACS Appl Mater Interfaces 2017 Sep 29;9(36):30958-30963. Epub 2017 Aug 29.

Key Laboratory of Polyoxometalate Science of the Ministry of Education, Faculty of Chemistry, Northeast Normal University , Changchun 130024, China.

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http://dx.doi.org/10.1021/acsami.7b10540DOI Listing
September 2017

Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015.

J Comput Aided Mol Des 2017 Aug 1;31(8):689-699. Epub 2017 Jul 1.

Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.

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http://dx.doi.org/10.1007/s10822-017-0038-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711532PMC
August 2017

THE ANTIBACTERIAL EFFECT OF . FROMV GUANGXI ON MICE WITH PNEUMONIA.

Afr J Tradit Complement Altern Med 2017 23;14(1):73-88. Epub 2016 Nov 23.

Regenerative medicine research center of Guangxi Medical University. Post Graduate Students.

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http://dx.doi.org/10.21010/ajtcam.v14i1.9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411887PMC
June 2017

Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions.

Proteins 2017 03 2;85(3):424-434. Epub 2016 Dec 2.

Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211, USA.

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http://dx.doi.org/10.1002/prot.25203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313341PMC
March 2017

Bevacizumab and wound-healing complications: a systematic review and meta-analysis of randomized controlled trials.

Oncotarget 2016 Dec;7(50):82473-82481

Pharmacy Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.

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http://dx.doi.org/10.18632/oncotarget.12666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5347706PMC
December 2016

Electrochemical Synthesis and Catalytic Properties of Encapsulated Metal Clusters within Zeolitic Imidazolate Frameworks.

Chemistry 2016 Nov 22;22(46):16613-16620. Epub 2016 Sep 22.

College of Chemistry, Jilin University, Changchun, 130012, P. R. China.

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http://dx.doi.org/10.1002/chem.201602924DOI Listing
November 2016

Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction.

Structure 2016 Oct 15;24(10):1842-1853. Epub 2016 Sep 15.

Department of Physics and Astronomy, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA; Department of Biochemistry, Informatics Institute, University of Missouri, Columbia, MO 65211, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080282PMC
http://dx.doi.org/10.1016/j.str.2016.07.021DOI Listing
October 2016

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Authors:
Marc F Lensink Sameer Velankar Andriy Kryshtafovych Shen-You Huang Dina Schneidman-Duhovny Andrej Sali Joan Segura Narcis Fernandez-Fuentes Shruthi Viswanath Ron Elber Sergei Grudinin Petr Popov Emilie Neveu Hasup Lee Minkyung Baek Sangwoo Park Lim Heo Gyu Rie Lee Chaok Seok Sanbo Qin Huan-Xiang Zhou David W Ritchie Bernard Maigret Marie-Dominique Devignes Anisah Ghoorah Mieczyslaw Torchala Raphaël A G Chaleil Paul A Bates Efrat Ben-Zeev Miriam Eisenstein Surendra S Negi Zhiping Weng Thom Vreven Brian G Pierce Tyler M Borrman Jinchao Yu Françoise Ochsenbein Raphaël Guerois Anna Vangone João P G L M Rodrigues Gydo van Zundert Mehdi Nellen Li Xue Ezgi Karaca Adrien S J Melquiond Koen Visscher Panagiotis L Kastritis Alexandre M J J Bonvin Xianjin Xu Liming Qiu Chengfei Yan Jilong Li Zhiwei Ma Jianlin Cheng Xiaoqin Zou Yang Shen Lenna X Peterson Hyung-Rae Kim Amit Roy Xusi Han Juan Esquivel-Rodriguez Daisuke Kihara Xiaofeng Yu Neil J Bruce Jonathan C Fuller Rebecca C Wade Ivan Anishchenko Petras J Kundrotas Ilya A Vakser Kenichiro Imai Kazunori Yamada Toshiyuki Oda Tsukasa Nakamura Kentaro Tomii Chiara Pallara Miguel Romero-Durana Brian Jiménez-García Iain H Moal Juan Férnandez-Recio Jong Young Joung Jong Yun Kim Keehyoung Joo Jooyoung Lee Dima Kozakov Sandor Vajda Scott Mottarella David R Hall Dmitri Beglov Artem Mamonov Bing Xia Tanggis Bohnuud Carlos A Del Carpio Eichiro Ichiishi Nicholas Marze Daisuke Kuroda Shourya S Roy Burman Jeffrey J Gray Edrisse Chermak Luigi Cavallo Romina Oliva Andrey Tovchigrechko Shoshana J Wodak

Proteins 2016 09 1;84 Suppl 1:323-48. Epub 2016 Jun 1.

Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1002/prot.25007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030136PMC
September 2016

Possible mechanism of PNS protection against cisplatin-induced nephrotoxicity in rat models.

Toxicol Mech Methods 2015 21;25(5):347-54. Epub 2015 May 21.

a Department of Pharmacy , the First Affiliated Hospital of Guangxi Medical University , Nanning , China.

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http://dx.doi.org/10.3109/15376516.2015.1006492DOI Listing
July 2016

Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks.

J Chem Inf Model 2016 06 1;56(6):1013-21. Epub 2015 Oct 1.

Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States.

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http://dx.doi.org/10.1021/acs.jcim.5b00504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130226PMC
June 2016

SM-TF: A structural database of small molecule-transcription factor complexes.

J Comput Chem 2016 06 24;37(17):1559-64. Epub 2016 Mar 24.

Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.

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http://dx.doi.org/10.1002/jcc.24370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4873394PMC
June 2016

Coupling fullerene into porous aromatic frameworks for gas selective sorption.

Chem Sci 2016 Jun 22;7(6):3751-3756. Epub 2016 Feb 22.

Key Laboratory of Polyoxometalate Science of the Ministry of Education , Faculty of Chemistry , Northeast Normal University , Changchun , 130024 , P. R. China . Email:

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http://xlink.rsc.org/?DOI=C6SC00134C
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http://dx.doi.org/10.1039/c6sc00134cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6008602PMC
June 2016

Electrochemical fabrication of copper-containing metal-organic framework films as amperometric detectors for bromate determination.

Dalton Trans 2016 05;45(18):7728-36

College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, Heilongjiang 150025, P. R. China.

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http://dx.doi.org/10.1039/c5dt04229aDOI Listing
May 2016

Panax notoginseng saponins attenuates cisplatin-induced nephrotoxicity via inhibiting the mitochondrial pathway of apoptosis.

Int J Clin Exp Pathol 2014 15;7(12):8391-400. Epub 2014 Nov 15.

Department of Pharmacy, The First Affiliated Hospital of Guangxi Medical University Nanning 530021, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4314003PMC
October 2015

Self-supported fibrous porous aromatic membranes for efficient CO2/N2 separations.

ACS Appl Mater Interfaces 2015 Jul 10;7(28):15561-9. Epub 2015 Jul 10.

‡Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China.

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http://dx.doi.org/10.1021/acsami.5b04148DOI Listing
July 2015

Computation and simulation of the structural characteristics of the kidney urea transporter and behaviors of urea transport.

J Phys Chem B 2015 Apr 27;119(16):5124-31. Epub 2015 Mar 27.

§Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States.

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http://dx.doi.org/10.1021/jp511300uDOI Listing
April 2015

Predicting peptide binding sites on protein surfaces by clustering chemical interactions.

J Comput Chem 2015 Jan 3;36(1):49-61. Epub 2014 Nov 3.

Department of Physics and Astronomy and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.

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http://doi.wiley.com/10.1002/jcc.23771
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http://dx.doi.org/10.1002/jcc.23771DOI Listing
January 2015

ITScorePro: an efficient scoring program for evaluating the energy scores of protein structures for structure prediction.

Methods Mol Biol 2014 ;1137:71-81

Department of Physics and Astronomy, Dalton Cardiovascular Research Center, Informatics Institute, University of Missouri, Columbia, MO, USA.

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http://dx.doi.org/10.1007/978-1-4939-0366-5_6DOI Listing
October 2014

Cholesterol biosynthesis inhibitors as potent novel anti-cancer agents: suppression of hormone-dependent breast cancer by the oxidosqualene cyclase inhibitor RO 48-8071.

Breast Cancer Res Treat 2014 Jul 31;146(1):51-62. Epub 2014 May 31.

Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.

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http://dx.doi.org/10.1007/s10549-014-2996-5DOI Listing
July 2014

Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design.

Molecules 2014 Jul 11;19(7):10150-76. Epub 2014 Jul 11.

Informatics Institute, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.3390/molecules190710150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6270832PMC
July 2014

Highly selective and permeable porous organic framework membrane for CO₂ capture.

Adv Mater 2014 Jun 20;26(22):3644-8. Epub 2014 Mar 20.

State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, China, 130012.

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http://dx.doi.org/10.1002/adma.201400020DOI Listing
June 2014

A Bayesian statistical approach of improving knowledge-based scoring functions for protein-ligand interactions.

J Comput Chem 2014 May 13;35(12):932-43. Epub 2014 Mar 13.

Informatics Institute, University of Missouri, Columbia, Missouri, 65211; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, 65211.

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http://dx.doi.org/10.1002/jcc.23579DOI Listing
May 2014

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method.

Nucleic Acids Res 2014 Apr 29;42(7):e55. Epub 2014 Jan 29.

Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1093/nar/gku077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985650PMC
April 2014

A chemical genetic approach demonstrates that MPK3/MPK6 activation and NADPH oxidase-mediated oxidative burst are two independent signaling events in plant immunity.

Plant J 2014 Jan 17;77(2):222-34. Epub 2013 Dec 17.

State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Division of Biochemistry, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.

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http://dx.doi.org/10.1111/tpj.12382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017028PMC
January 2014

Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI).

Proteins 2013 Dec 14;81(12):2183-91. Epub 2013 Nov 14.

Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, Informatics Institute, University of Missouri, Columbia, Missouri, 65211.

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http://dx.doi.org/10.1002/prot.24435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916956PMC
December 2013

Eco-friendly fabrication of hydrophilic ZSM-5 membranes for alcohol upgrading.

Chem Commun (Camb) 2013 Oct;49(78):8839-41

State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, China130012.

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http://dx.doi.org/10.1039/c3cc44515aDOI Listing
October 2013

Automated large-scale file preparation, docking, and scoring: evaluation of ITScore and STScore using the 2012 Community Structure-Activity Resource benchmark.

J Chem Inf Model 2013 Aug 21;53(8):1905-14. Epub 2013 May 21.

Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1021/ci400045vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755023PMC
August 2013

Environmentally friendly synthesis of highly hydrophobic and stable MIL-53 MOF nanomaterials.

Chem Commun (Camb) 2013 Aug;49(67):7430-2

State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, China 130012.

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http://xlink.rsc.org/?DOI=c3cc42287a
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http://dx.doi.org/10.1039/c3cc42287aDOI Listing
August 2013

Topology-directed design of porous organic frameworks and their advanced applications.

Chem Commun (Camb) 2013 May 19;49(38):3925-36. Epub 2013 Mar 19.

State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, China.

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http://dx.doi.org/10.1039/c3cc00039gDOI Listing
May 2013

A nonredundant structure dataset for benchmarking protein-RNA computational docking.

J Comput Chem 2013 Feb 10;34(4):311-8. Epub 2012 Oct 10.

Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1002/jcc.23149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546201PMC
February 2013

Influences of mutations on the electrostatic binding free energies of chloride ions in Escherichia coli ClC.

J Phys Chem B 2012 Jun 29;116(22):6431-8. Epub 2012 May 29.

Department of Physics, Wuhan University, Wuhan 430072, PR China.

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http://dx.doi.org/10.1021/jp300430fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411325PMC
June 2012

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

J Mol Biol 2011 Nov 29;414(2):289-302. Epub 2011 Sep 29.

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

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http://kiharalab.org/web/paper/communitywidecapri_JMB2011.pd
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http://linkinghub.elsevier.com/retrieve/pii/S002228361101055
Publisher Site
http://dx.doi.org/10.1016/j.jmb.2011.09.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839241PMC
November 2011

Co3(HCOO)6 microporous metal-organic framework membrane for separation of CO2/CH4 mixtures.

Chemistry 2011 Oct 16;17(43):12076-83. Epub 2011 Sep 16.

Laboratoire Catalyse & Spectrochimie, ENSICAEN, Université de Caen, CNRS, 6 Boulevard du Marechal Juin, 14050 Caen, France.

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http://dx.doi.org/10.1002/chem.201101733DOI Listing
October 2011

Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures.

Proteins 2011 Sep 5;79(9):2648-61. Epub 2011 Jul 5.

Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1002/prot.23086DOI Listing
September 2011

Construction and test of ligand decoy sets using MDock: community structure-activity resource benchmarks for binding mode prediction.

J Chem Inf Model 2011 Sep 3;51(9):2107-14. Epub 2011 Aug 3.

Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States.

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http://dx.doi.org/10.1021/ci200080gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190646PMC
September 2011

Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function.

J Chem Inf Model 2011 Sep 31;51(9):2097-106. Epub 2011 Aug 31.

Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States.

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http://dx.doi.org/10.1021/ci2000727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3190652PMC
September 2011

An inverse docking approach for identifying new potential anti-cancer targets.

J Mol Graph Model 2011 Apr 19;29(6):795-9. Epub 2011 Jan 19.

Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, United States.

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http://dx.doi.org/10.1016/j.jmgm.2011.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068237PMC
April 2011

Binding of ATP to the CBS domains in the C-terminal region of CLC-1.

J Gen Physiol 2011 Apr;137(4):357-68

Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA.

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http://dx.doi.org/10.1085/jgp.201010495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068280PMC
April 2011

MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19.

Proteins 2010 Nov;78(15):3096-103

Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211, USA.

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http://doi.wiley.com/10.1002/prot.22797
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952710PMC
November 2010

Coronary microvascular dysfunction in diabetes mellitus: A review.

World J Cardiol 2010 Nov;2(11):377-90

Andrea Picchi, Marta Focardi, Ji-Min Cao, Department of Cardiology, Misericordia Hospital, Via Senese 161, 58100 Grosseto, Italy.

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http://dx.doi.org/10.4330/wjc.v2.i11.377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006474PMC
November 2010

Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

Phys Chem Chem Phys 2010 Oct 23;12(40):12899-908. Epub 2010 Aug 23.

Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1039/c0cp00151aDOI Listing
October 2010

Ion sensing in the RCK1 domain of BK channels.

Proc Natl Acad Sci U S A 2010 Oct 11;107(43):18700-5. Epub 2010 Oct 11.

Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Washington University, St. Louis, MO 63130, USA.

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http://dx.doi.org/10.1073/pnas.1010124107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2972974PMC
October 2010

Advances and challenges in protein-ligand docking.

Int J Mol Sci 2010 Aug 18;11(8):3016-34. Epub 2010 Aug 18.

Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA; Email:

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http://dx.doi.org/10.3390/ijms11083016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996748PMC
August 2010

Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions.

J Chem Inf Model 2010 Feb;50(2):262-73

Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1021/ci9002987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199178PMC
February 2010

Multiscale generalized born modeling of ligand binding energies for virtual database screening.

J Phys Chem B 2009 Sep;113(35):11793-9

Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1021/jp901212tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763608PMC
September 2009

Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach.

J Mol Graph Model 2009 Apr 24;27(7):822-8. Epub 2008 Dec 24.

Dalton Cardiovascular Research Center, Department of Physics & Astronomy, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1016/j.jmgm.2008.12.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758335PMC
April 2009

Synthesis of a metal-organic framework film by direct conversion technique for VOCs sensing.

Dalton Trans 2009 Apr 10(16):3009-13. Epub 2009 Mar 10.

State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, P. R. China.

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http://dx.doi.org/10.1039/b822248gDOI Listing
April 2009

Cutoff variation induces different topological properties: a new discovery of amino acid network within protein.

J Theor Biol 2009 Feb 1;256(3):408-13. Epub 2008 Nov 1.

Department of Physics, Wuhan University, Wuhan 430072, China.

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http://dx.doi.org/10.1016/j.jtbi.2008.09.042DOI Listing
February 2009

An iterative knowledge-based scoring function for protein-protein recognition.

Proteins 2008 Aug;72(2):557-79

Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1002/prot.21949DOI Listing
August 2008

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.

Proteins 2007 Feb;66(2):399-421

Dalton Cardiovascular Research Center and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1002/prot.21214DOI Listing
February 2007

Efficient molecular docking of NMR structures: application to HIV-1 protease.

Protein Sci 2007 Jan 22;16(1):43-51. Epub 2006 Nov 22.

Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1110/ps.062501507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2222846PMC
January 2007

An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function.

J Comput Chem 2006 Nov;27(15):1876-82

Department of Biochemistry, Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1002/jcc.20505DOI Listing
November 2006

An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials.

J Comput Chem 2006 Nov;27(15):1866-75

Department of Biochemistry, Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1002/jcc.20504DOI Listing
November 2006

Similarities and differences between organic cation inhibition of the Na,K-ATPase and PMCA.

Biochemistry 2006 Nov;45(44):13331-45

Division of Biomedical Sciences, Department of Biological Sciences, Illinois State University, Normal, Illinois 61790-4120, USA.

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http://dx.doi.org/10.1021/bi060667jDOI Listing
November 2006

The two ATP binding sites of cystic fibrosis transmembrane conductance regulator (CFTR) play distinct roles in gating kinetics and energetics.

J Gen Physiol 2006 Oct 11;128(4):413-22. Epub 2006 Sep 11.

Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO 65211, USA.

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http://www.jgp.org/lookup/doi/10.1085/jgp.200609622
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2151577PMC
October 2006

Hierarchical growth of large-scale ordered zeolite silicalite-1 membranes with high permeability and selectivity for recycling CO2.

Angew Chem Int Ed Engl 2006 Oct;45(42):7053-6

State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, China.

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http://dx.doi.org/10.1002/anie.200602308DOI Listing
October 2006

Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach.

J Phys Chem B 2006 May;110(18):9304-13

Dalton Cardiovascular Research Center and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.

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http://dx.doi.org/10.1021/jp060334wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716126PMC
May 2006

High affinity ATP/ADP analogues as new tools for studying CFTR gating.

J Physiol 2005 Dec 13;569(Pt 2):447-57. Epub 2005 Oct 13.

Department of Medical Pharmacology, University of Missouri-Columbia, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1113/jphysiol.2005.095083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464241PMC
December 2005

CFTR gating II: Effects of nucleotide binding on the stability of open states.

J Gen Physiol 2005 Apr 14;125(4):377-94. Epub 2005 Mar 14.

Department of Medical Pharmacology and Physiology, University of Missouri-Columbia 65211, USA.

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http://dx.doi.org/10.1085/jgp.200409228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1289160PMC
April 2005

Detailed kinetic studies of an aggregating inhibitor; inhibition of phosphomannomutase/phosphoglucomutase by disperse blue 56.

Biochemistry 2004 Jul;43(27):8662-9

Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, USA.

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http://pubs.acs.org/doi/abs/10.1021/bi0491907
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July 2004