Publications


Xu X, Kao WL, Wang A, Lee HJ, Duan R, Holmes H, Gallazzi F, Ji J, Sun H, Heng X, Zou X.
In silico screening of protein-binding peptides with an application to developing peptide inhibitors against antibiotic resistance.
PNAS Nexus, 3(12): pgae541, 2024. [Link]

2023

Xu X1, Duan R1, Zou X.
Template-guided method for protein-ligand complex structure prediction: Application to CASP15 protein-ligand studies.
Proteins, 91(12): 1829-1836, 2023. [Link]

Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ.
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.
Proteins, 91(12): 1658-1683, 2023. [Link]

Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, Lheritier A, Fernandez-Recio J, Rodriguez-Lumbreras LA, Schueler-Furman O, Varga JK, Jimenez-Garcia B, Reau MF, Bonvin AMJJ, Savojardo C, Martelli PL, Casadio R, Tubiana J, Wolfson HJ, Oliva R, Barradas-Bautista D, Ricciardelli T, Cavallo L, Venclovas C, Olechnovic K, Guerois R, Andreani J, Martin J, Wang X, Terashi G, Sarkar D, Christoffer C, Aderinwale T, Verburgt J, Kihara D, Marchand A, Correia BE, Duan R, Qiu L, Xu X, Zhang S, Zou X, Dey S, Dunbrack RL, Levy ED, Wodak SJ.
Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.
Proteomics, 23(17): e2200323, 2023. [Link]

Shi-Jie Chen, Mubashir Hassan, Robert L. Jernigan, Kejue Jia, Daisuke Kihara, Andrzej Kloczkowski, Sergei Kotelnikov, Dima Kozakov, Jie Liang, Adam Liwo, Silvina Matysiak, Jarek Meller, Cristian Micheletti, Julie C Mitchell, Sayantan Mondal, Ruth Nussinov, Kei-ichi Okazaki, Dzmitry Padhorny, Jeffrey Skolnick, Tobin S. Sosnick, George Stan, Ilya Vakser, Xiaoqin Zou, and George D. Rose
Opinion: Protein folds vs. protein folding: Differing questions, different challenges.
Proceedings of the National Academy of Sciences 120(1): e2214423119, 2023. [Link]

G Zane, M Silveria, N Meyer, T White, R Duan, X Zou, M Chapman.
Cryo-EM structure of adeno-associated virus 4 at 2.2 A resolution.
Acta Crystallographica Section D: Structural Biology 79(2): 140-153, 2023. [Link]

2022

Zhang G1, Xu X1, Jia Z1, Geng Y, Liang H, Shi J, Marras M, Abella A, Magleby KL, Silva JR*, Chen J*, Zou X*, Cui J*.
An allosteric modulator activates BK channels by perturbing coupling between Ca2+ binding and pore opening.
Nature Communications, 13: 6784, 2022. [Link]

Xu X, Zou X.
Predicting protein-peptide complex structures by accounting for peptide flexibility and physicochemical environment.
Journal of Chemical Information and Modeling, 62: 27-39, 2022. [Link]

Cheng Y, Zhang D, Hurst T, Zou X, Giangrande PH, Chen SJ.
RNA structural modeling for therapeutic applications.
Invited book chapter in RNA Nanotechnology and Therapeutics Second Edition. Peixuan Guo and Kirill A. Afonin (eds.), CRC Press, Florida, 2022. ISBN 9781138312869

Qiu L, Bhutoria S, Kalpana GV, Zou X.
Computational Modeling of IN-CTD/TAR Complex to Elucidate Additional Strategies to Inhibit HIV-1 Replication.
Virus-Host Interactions: Methods and Protocols, 75-84, 2022.

2021

Xu X, Zou X.
Dissimilar Ligands Bind in a Similar Fashion: A Guide to Ligand Binding-Mode Prediction with Application to CELPP Studies.
International Journal of Molecular Sciences, 22(22): 12320, 2021. [Link]

Lin Y1, Grinter SZ1, Lu Z1, Xu X1, Wang HZ, Liang H, Hou P, Gao J, Clausen C, Shi J, Zhao W, Ma Z, Liu Y, White KM, Zhao L, Kang PW, Zhang G, Cohen IS*, Zou X*, Cui J*.
Modulating the voltage sensor of a cardiac potassium channel shows antiarrhythmic effects.
Proceedings of the National Academy of Sciences, 118(20): e2024215118, 2021. [Link]
In the News: Compound may prevent risk of a form of arrhythmia from common medications

Li M, Xu X, Zou X, Hazelbauer GL.
A Selective Tether Recruits Activated Response Regulator CheB to Its Chemoreceptor Substrate.
Mbio 12(6): e03106-21, 2021. [Link]

Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Gieldon A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Slusarz R, Wesolowski PA, Zieba K, Del Carpio Munoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jimenez-Garcia B, Koukos PI, Van Keulen S, Van Noort CW, Reau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodriguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkunas J, Olechnovic K, Venclovas C, Duan R, Qiu L, Xu X, Zhang S, Zou X, Wodak SJ.
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.
Proteins: Structure, Function, and Bioinformatics, 89(12): 1800-1823, 2021. [Link]

Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X.
The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity.
Nucleic acids research, 49(10): 5925-5942, 2021. [Link]

Dixit U, Bhutoria S, Wu X, Qiu L, Spira M, Mathew S, Harris R, Adams LJ, Cahill S, Pathak R, Kumar PR, Nguyen M, Acharya SA, Brenowitz M, Almo SC, Zou X, Steven AC, Cowburn D, Girvin M, Kalpana GV.
Nature communications, 12: 2743, 2021. [Link]

Ma Z, Huang SY, Cheng F, Zou X.
Rapid Identification of Inhibitors and Prediction of Ligand Selectivity for Multiple Proteins: Application to Protein Kinases.
The Journal of Physical Chemistry B, 125(9): 2288-2298, 2021. [Link]

Ma Z, Zou X.
MDock: A Suite for Molecular Inverse Docking and Target Prediction.
Methods in Molecular Biology (Clifton, NJ), 2266: 313-322, 2021. [Link]

Zhang S, Chen KY, Zou X.
Carbohydrate-protein interactions: advances and challenges.
Communications in Information and Systems, 21 (1): 147-163, 2021. [Link]

2020

Liu Y1, Xu X1, Gao J1, Naffaa MM, Liang H, Shi J, Wang HZ, Yang ND, Hou P, Zhao W, White KM, Kong W, Dou A, Cui A, Zhang G, Cohen IS*, Zou X*, Cui J*.
A PIP 2 substitute mediates voltage sensor-pore coupling in KCNQ activation.
Communications Biology, 3: 1-12, 2020. [Link]


Duan R1, Qiu L1, Xu X1, Ma Z1, Merideth BR, Shyu CR, Zou X.
Performance of Human and Server Prediction in CAPRI rounds 38-45.
Proteins: Structure, Function, and Bioinformatics, 88(8): 1110-1120, 2020. [Link]


Ptacek J, Zhang D, Qiu L, Kruspe S, Motlova L, Kolenko P, Novakova Z, Shubham S, Havlinova B, Baranova P, Chen SJ, Zou X, Giangrande P, Barinka C.
Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer.
Nucleic Acids Research, 48 (19): 11130-11145, 2020. [Link]


Nguyen PD, Zheng J, Gremminger TJ, Qiu L, Zhang D, Tuske S, Lange MJ, Griffin PR, Arnold E, Chen SJ, Zou X, Heng X, Burke D.
Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase.
Nucleic Acids Research, 48: 2709-2722, 2020. [Link]


Zhou X, Park KH, Yamazaki D, Lin PH, Nishi M, Ma Z, Qiu L, Murayama T, Zou X, Takeshima H, Zhou J, Ma J.
TRIC-A channel maintains store calcium handling by interacting with type 2 ryanodine receptor in cardiac muscle.
Circulation Research, 126: 417-435, 2020. [Link]


Hou P, Kang PW, Kongmeneck AD, Yang ND, Liu Y, Shi J, Xu X, White KM, Zaydman MA, Kasimova MA, Seebohm G, Zhong L, Zou X, Tarek M, Cui J.
Two-stage electro-mechanical coupling of a KV channel in voltage-dependent activation.
Nature Communications, 11: 676, 2020. [Link]


Xu X, Zou X.
MDockPeP: A Web Server for Blind Prediction of Protein-Peptide Complex Structures.
Protein Structure Prediction, 259-272, 2020. [Link]


Qiu L, Zou X.
Scoring functions for protein-RNA complex structure prediction: advances, applications, and future directions.
Communications in Information and Systems, 20: 1-22, 2020. ptide-protein computational docking. [Link]


Xu X, Zou X.
PepPro: a non-redundant structure data set for benchmarking peptide-protein computational docking.
Journal of Computational Chemistry, 41: 362-369, 2020. [Link]
[Link to PepPro dataset]

2019

Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon L, Samsonov S, Liwo A, Crivelli S, Pages G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodriguez-Lumbreras LA, Romero-Durana M, Diaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchene I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkunas J, Olechnovic K, Venclovas C, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Merideth BR, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jimenez-Garcia B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ.
Blind prediction of homo-and hetero-protein complexes: The CASP13-CAPRI experiment.
Proteins: Structure, Function and Bioinformatics, 2019. https://doi.org/10.1002/prot.25838

Yeh HI, Qiu L, Sohma Y, Conrath K, Zou X*, Hwang TC*.
Identifying the molecular target sites for CFTR potentiators GLPG1837 and VX-770.
Journal of General Physiology, 151: 912-928, 2019. [link]

Xu X1, Ma Z1, Duan R1, Zou X.
Predicting protein-ligand binding modes for CELPP and GC3: workflows and insight.
Journal of Computer-Aided Molecular Design, 33: 367-374, 2019. [link]

2018

Xu X1, Yan C1, Zou X.
MDockPeP: An ab-initio protein-peptide docking server.
Journal of Computational Chemistry, 39: 2409-2413, 2018. [link]

Xu X, Huang M, Zou X.
Docking-based inverse virtual screening: methods, applications, and challenges.
Biophysics Reports, 4: 1-16, 2018. (Awarded as the excellent paper of Biophysics Reports during 2018-2020) [link]

Duan R1, Xu X1, Zou X.
Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor.
Journal of Computer-Aided Molecular Design,32: 103-111, 2018. [link]

2017

Yan C, Zou X.
Modeling Protein Flexibility in Molecular Docking.
In: Samuel Chackalamannil, David P Rotella and Simon E Ward, (eds.) Comprehensive Medicinal Chemistry III vol. 3, pp. 319-328. Oxford: Elsevier, 2017. [link]

Xu X, Yan C, Zou X.
Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015.
Journal of Computer-Aided Molecular Design, 31: 689-699, 2017. [link]

Zhang HT, Wang Z, Yu T, Sang JP, Zou XW, Zou X.
Modeling of flux, binding and substitution of urea molecules in the urea transporter dvUT.
Journal of Molecular Graphics and Modelling, 76: 504-511, 2017. [link]

Yan C, Xu X, Zou X.
The Usage of ACCLUSTER for Peptide Binding Site Prediction.
Modeling Peptide-Protein Interactions: Methods and Protocols, 3-9, 2017. [link]

Xu X1, Qiu L1, Yan C1, Ma Z, Grinter SZ, Zou X.
Performance of MDockPP in CAPRI Rounds 28-29 and 31-35 including the prediction of water-mediated interactions.
Proteins, Special issue on 6th CAPRI Evaluations, 85: 424-434, 2017. [link]

2016

Yan C1, Xu X1, Zou X.
Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction.
Structure, 24: 1842-1853, 2016. [link]

Lensink MF, ..., Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, ...,Wodak SJ.
Prediction of homo-and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment.
Proteins, 84: 323-348, 2016. [link]

Yan C, Zou X.
MDock: An ensemble docking suite for molecular docking, scoring and in silico screening.
Methods in Pharmacology and Toxicology, pp 1-14, 2016. [link]

Xu X, Ma Z, Sun H, Zou X.
SM-TF: A structural database of small molecule-transcription factor complexes.
Journal of Computational Chemistry, 37: 1559-1564, 2016. [link]

2015
Yan C, Grinter SZ,Merideth BR, Ma Z, Zou XQ.
Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks.
Journal of Chemical Information and Modeling, 56: 1013-1021, 2015.

Wang Z, Yu T, Sang J-P, Zou X-W, Yan C, Zou XQ.
Computation and simulation of the structural and functional characteristics of the kidney urea transporter.
Journal of Physical Chemistry B, 119: 5124-5131, 2015.
(featured in the front cover of the issue)

Yan C, Zou XQ.
Predicting peptide binding sites on protein surfaces by clustering chemical interactions.
Journal of Computational Chemistry, 36: 49-61, 2015.
(featured in the inside cover of the issue).

2014
Grinter SZ, Zou XQ.
Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design.
Molecules, 19(7), 10150-10176, 2014.

Grinter SZ, Zou XQ.
A Bayesian statistical approach of improving knowledge-based scoring functions for protein-ligand interactions.
Journal of Computational Chemistry, 35: 932-943, 2014.
(featured in the front cover of the issue).

Huang SY, Zou XQ.
A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method.
Nucleic Acids Research, 1-12, doi:10.1093/nar/gku077, 2014.

Huang SY, Zou XQ.
ITScorePro - An efficient scoring program for evaluating the energy scores of protein structures for structure prediction.
Methods in Molecular Biology, Protein Structure Prediction (3rd Edition), Daisuke Kihara (ed.), Chapter 6, Springer Science + Business Media, New York, 2014.

Li M, Chang S, Shi J, McFarland K, Yang L, Yang X, Moller A, Wang C, Zou XQ, Chi C, Cui J.
Conopeptide Vt3.1 preferentially inhibits BK potassium channels containing beta4 subunits via electrostatic interactions.
Journal of Biological Chemistry, 289: 4735-4742, 2014.

Xu J, Jie X, Yan C, Zou XQ, Ren D, Zhang S.
A chemical genetic approach demonstrates that MPK3/MPK6 activation and NADPH oxidase-mediated oxidative burst are two independent signaling events in plant immunity.
Plant Journal, 77: 222-234, 2014.

Lensink MF, ..., Huang SY, Zou XQ, Wojdyla JA, Kleanthous C, Wodak SJ.
Blind Prediction of Interfacial Water Positions in CAPRI.
Proteins: Structure, Function and Bioinformatics, 82:620-32, 2014.

2013
Huang SY, Yan C, Grinter SZ, Chang S, Jiang L, Zou XQ.
Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in CAPRI.
Proteins: Structure, Function and Bioinformatics, Special issue on 5th CAPRI Evaluations,81: 2183-2191, 2013.

Grinter SZ, Yan C, Huang SY, Jiang L, Zou XQ.
Automated large-scale file preparation, docking, and scoring: Evaluation of ITScore and STScore using the 2012 Community Structure-Activity Resource Benchmark.
Journal of Chemical Information and Modeling, Special issue on CSAR 2012 Scoring Exercise, 53:1905-1914, 2013.

Huang SY, Zou XQ.
A non-redundant structure dataset for benchmarking protein-RNA computational docking.
Journal of Computational Chemistry, 34:311-318, 2013 (featured in the front cover of the issue).

Moretti R, ..., Huang SY, Zou XQ, Velankar S, Janin J, Wodak SJ, Baker D.
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Proteins: Structure, Function and Bioinformatics, 81:1980-1987, 2013.

2012
Tao Yu, Xiao-Qing Wang, Jian-Ping Sang, Chun-Xu Pan, Xian-Wu Zou, Tsung-Yu Chen, Zou XQ.
Influences of mutations on the electrostatic binding free energies.
Journal of Physical Chemistry B, 116:6431-6438, 2012.

2011
Huang SY, Zou XQ.
Construction and test of ligand decoy sets using MDock: Community Structure-Activity Resource benchmarks for binding mode prediction.
Journal of Chemical Information and Modeling, Special issue on CSAR 2010 Scoring Exercise, 51:2107-2114, 2011.

Huang SY, Zou XQ.
Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function.
Journal of Chemical Information and Modeling, Special issue on CSAR 2010 Scoring Exercise,51:2097-2106, 2011.

Huang SY, Zou XQ.
Statistical mechanics-based energy scoring function for structural model selection in protein structure prediction.
Proteins: Structure, Function and Bioinformatics, 79:2648-2661, 2011.

Rockey MW, Hernandez FJ, Huang SY, Cao S, Howell CA, Thomas GS, Liu XY, Lapteva N, Spencer DM, McNamara JO II, Zou XQ, Chen SJ, Giangrande PH.
Rational truncation of an RNA aptamer to prostate specific membrane antigen using computational structural modeling.
Nucleic Acid Therapeutics, 21:299-314, 2011.

Fleishman SJ, ..., Huang SY, Zou XQ, Wodak SJ, Janin J, Baker D.
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
Journal of Molecular Biology,414:289-302, 2011.

Grinter SZ, Liang YY, Huang SY, Hyder SM, Zou XQ.
An inverse docking approach for identifying new potential anti-cancer targets.
Journal of Molecular Graphics and Modelling, 29: 795-799, 2011.

Tseng P-Y, Yu W-P, Liu HY, Zhang X-D, Zou XQ, Chen T-Y.
Binding of ATP to the CBS domains in the carboxyl-terminal region of CLC-1.
Journal of General Physiology, 137:357-368, 2011.

2010
Huang SY, Zou XQ.
A hierarchical approach to protein-protein docking and its application to CAPRI rounds 15-19.
Proteins: Structure, Function and Bioinformatics, Special Issue on 4th CAPRI Evaluations, 78:3096-3103, 2010.

Huang SY, Grinter SZ, Zou XQ.
Scoring functions for protein-ligand docking: recent advances and future directions.
Physical Chemistry Chemical Physics (invited perspective), 12: 12899-12908, 2010.

Zhang GH, Huang S-Y, Yang JQ, Shi JY, Yang X, Moller A, Zou XQ, Cui JM.
Ion sensing in the RCK1 domain of BK channels.
Proceedings of National Academy of Sciences USA, 107:18700-5, 2010.

Picchi A, Capobianco S, Qiu TY, Focardi M, Zou XQ, Cao J-M, Zhang, CH.
Coronary microvascular dysfunction in diabetes mellitus: a review.
World Journal of Cardiology (invited review), 2: 377-390, 2010.

Huang SY, Zou XQ.
Mean-force scoring functions for protein-ligand binding.
Annual Reports in Computational Chemistry (invited book chapter), Volume 6, Chapter 14, 281-296, 2010.

Wang X-Q, Yu T, Sang J-P, Zou X-W, Chen T-Y, Bolser D, Zou XQ.
A three-state multi-Ion kinetic model for conduction properties of ClC-0 chloride channel.
Biophysical Journal, 99: 464-471, 2010.

Huang SY, Zou XQ.
Recent advances and future directions for protein-ligand docking.
International Journal of Molecular Sciences, Special Issue 73: "Advances in Molecular Recognition" (invited review),11: 3016-3034, 2010.

Huang SY, Zou XQ.
Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions.
Journal of Chemical Information and Modeling, 50:262-273, 2010.

2009
Liu HY, Grinter S, Zou XQ.
Multiscale generalized Born modeling of ligand binding energies for virtual database screening.
Journal of Physical Chemistry B, 113:11793-1799, 2009.

Huang SY, Bolser D, Liu HY, Hwang TC, Zou XQ.
Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach.
Journal of Molecular Graphics and Modelling, 27: 822-828, 2009.

Tao Y, Zou XQ, Huang SY, Zou X-W.
Cutoff variation induces different topological properties: A new discovery of amino acid network within protein.
Journal of Theoretical Biology,256: 408-13, 2009.

2008
Huang SY, Zou XQ.
An iterative knowledge-based scoring function for protein-protein recognition.
Proteins: Structure, Function and Bioinformatics, 72:557-579, 2008.

Zhang LQ, Adyshev DM, Singleton P, Li HL, Cepeda J, Huang SY, Zou XQ, Verin AD, Tu JC, Garcia JGN, Ye SQ.
Interactions between PBEF and oxidative stress proteins - A potential new mechanism underlying PBEF in the pathogenesis of acute lung injury.
FEBS LETTERS, 582: 1802-1808, 2008.

2007
Huang SY, Zou XQ.
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking.
Proteins: Structure, Function and Bioinformatics, 66:399-421, 2007.

Huang SY, Zou XQ.
Efficient molecular docking of NMR structures: Application to HIV-1 protease.
Protein Science, 16:43-51, 2007.

2006
Gatto C, Helms JB, Prasse MC, Huang SY, Zou XQ, Arnett KL, Milanick MA.s
Similarities and differences between organic cation inhibition of the Na,K-ATPase and PMCA.
Biochemistry, 45:13331-13345, 2006.

Huang SY, Zou XQ.
An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials.
Journal of Computational Chemistry, 27:1866-1875, 2006.

Huang SY, Zou XQ.
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function.
Journal of Computational Chemistry, 27:1876-1882, 2006.

Zhou Z, Wang XH, Liu HY, Zou XQ, Li M, Hwang TC.
The two ATP binding sites of cystic fibrosis transmembrane conductance regulator (CFTR) play distinct roles in gating kinetics and energetics.
Journal of General Physiology, 128: 413-422, 2006.

Liu HY, Zou XQ.
Electrostatics of ligand binding: Parametrization of the generalized born model and comparison with the Poisson-Boltzmann approach.
Journal of Physical Chemistry B, 110: 9304-9313, 2006.

2005-
Zhou Z, Wang XH, Li M, Zou XQ, Hwang TC.
High affinity ATP/ADP analogues as new tools for studying CFTR gating.
JOURNAL OF PHYSIOLOGY-LONDON, 569: 447-457, 2005.

Bompadre SG, Cho JH, Wang XH, Zou XQ, Sohma Y, Li M, Hwang TC.
High affinity ATP/ADP analogues as new tools for studying CFTR gating.
JOURNAL OF PHYSIOLOGY-LONDON,569: 447-457, 2005.

Liu HY, Wang XH, Regni C, Zou XQ, Tipton PA.
Detailed kinetic studies of an aggregating inhibitor; Inhibition of phosphomannomutase/ phosphoglucomutase by Disperse Blue 56.
BIOCHEMISTRY, 43:8662-8669, 2004.

Liu HY, Kuntz ID, Zou XQ.
Pairwise GB/SA scoring function for structure-based drug design.
JOURNAL OF PHYSICAL CHEMISTRY B, 108:5453-5462, 2004.

Zou XQ, Hwang TC.
ATP hydrolysis-coupled gating of CFTR chloride channels: Structure and function.
BIOCHEMISTRY, 40:5579-5586, 2001.

Lamb ML, Burdick KW, Toba S, Young MM, Skillman KG, Zou XQ, Arnold JR, Kuntz ID.
Design, docking, and evaluation of multiple libraries against multiple targets.
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 42:296-318, 2001.

Zou XQ, Sun YX, Kuntz ID.
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