Importance of protein flexibility on molecular recognition: modeling binding mechanisms of aminopyrazine inhibitors to Nek2

Xinyi Tang, Zhe Wang, Tailong Lei, Wenfang Zhou, Shan Chang and Dan Li

Phys. Chem. Chem. Phys., 2018, 20, 5591
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Computational insights into different inhibition modes of the κ-opioid receptor with antagonists LY2456302 and JDTic

Jianxin Cheng, Weihua Li, Guixia Liu, Weiliang Zhu and Yun Tang

RSC Adv., 2016, 6, 13626
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Use multiscale simulation to explore the effects of the homodimerizations between different conformation states on the activation and allosteric pathway for the μ-opioid receptor

Xi Zhang, Yuan Yuan, Longrong Wang, Yanzhi Guo, Menglong Li, Chuan Li and Xuemei Pu

Phys. Chem. Chem. Phys., 2018, 20, 13485
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Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD

Anna S. Kamenik, Ursula Kahler, Julian E. Fuchs and Klaus R. Liedl

J. Chem. Theory Comput., 2016, 12, 3449
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Substrate-Specific Screening for Mutational Hotspots Using Biased Molecular Dynamics Simulations

Maximilian C. C. J. C. Ebert, Joaquin Guzman Espinola, Guillaume Lamoureux and Joelle N. Pelletier

ACS Catal., 2017, 7, 6786
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Discovery of potential PARP7 cyclic peptide inhibitors by De novo design and optimization

Yuqi Zhu, Aamir Mehmood and Daixi Li

Computational and Theoretical Chemistry, 2025, 1254, 115438
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Molecular Mechanism Regarding Allosteric Modulation of Ligand Binding and the Impact of Mutations on Dimerization for CCR5 Homodimer

Fuhui Zhang, Yuan Yuan, Minghui Xiang, Yanzhi Guo, Menglong Li, Yijing Liu and Xuemei Pu

J. Chem. Inf. Model., 2019, 59, 1965
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The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation

Jeevan B. GC, Bernard S. Gerstman and Prem P. Chapagain

J. Phys. Chem. B, 2015, 119, 12750
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Towards Selective Binding to the GLUT5 Transporter: Synthesis, Molecular Dynamics and In Vitro Evaluation of Novel C-3-Modified 2,5-Anhydro-D-mannitol Analogs

Natasha Rana, Marwa A. Aziz, Ahmed K. Oraby, Melinda Wuest, Jennifer Dufour, Khaled A. M. Abouzid, Frank Wuest and F. G. West

Pharmaceutics, 2022, 14, 828
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Computational study of the structural ensemble of CC chemokine receptor type 5 (CCR5) and its interactions with different ligands

Guillermo Goode-Romero, Laura Dominguez and L. Michel Espinoza-Fonseca

PLoS ONE, 2022, 17, e0275269
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Insights into the structure–function relationship of both wild and mutant zinc transporter ZnT8 in human: a computational structural biology approach

Manoj Kumar Gupta and Ramakrishna Vadde

Journal of Biomolecular Structure and Dynamics, 2020, 38, 137
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Probing the Druggablility on the Interface of the Protein–Protein Interaction and Its Allosteric Regulation Mechanism on the Drug Screening for the CXCR4 Homodimer

Liting Shen, Yuan Yuan, Yanzhi Guo, Menglong Li, Chuan Li and Xuemei Pu

Front. Pharmacol., 2019, 10
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Conformation Transition of Intracellular Part of Glucagon Receptor in Complex With Agonist Glucagon by Conventional and Accelerated Molecular Dynamics Simulations

Qifeng Bai, Shuoyan Tan, Horacio Pérez-Sánchez, Haixia Feng, Liya Feng, HuanXiang Liu and Xiaojun Yao

Front. Chem., 2019, 7
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Frequency and Env determinants of HIV-1 subtype C strains from antiretroviral therapy-naive subjects that display incomplete inhibition by maraviroc

Katharina Borm, Martin R. Jakobsen, Kieran Cashin, Jacqueline K. Flynn, Paula Ellenberg, Lars Ostergaard, Benhur Lee, Melissa J. Churchill, Michael Roche and Paul R. Gorry

Retrovirology, 2016, 13
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Computational studies on horseshoe shape pocket of human orexin receptor type 2 and boat conformation of suvorexant by molecular dynamics simulations

Qifeng Bai, Horacio Pérez‐Sánchez, Zhuoyu Shi, Lanlan Li, Danfeng Shi, Huanxiang Liu and Xiaojun Yao

Chem Biol Drug Des, 2018, 92, 1221
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A Computational Study on the Blocking Ability of Selected Commercially Available Anticancer Drugs and Their Hypothetic Derivatives on the CCR5

Rahim Ghadari and Yousef Mohammadzadeh

ASSAY and Drug Development Technologies, 2018, 16, 266
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Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

Qifeng Bai and Xiaojun Yao

Sci Rep, 2016, 6
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Computational study on the inhibition mechanism of a cyclic peptide MaD5 to PfMATE: Insight from molecular dynamics simulation, free energy calculation and dynamical network analysis

Xiaojie Jin, Qifeng Bai, Weiwei Xue, Huanxiang Liu and Xiaojun Yao

Chemometrics and Intelligent Laboratory Systems, 2015, 149, 81
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Binding Kinetics and Pathways of Ligands to GPCRs

Andrea Strasser, Hans-Joachim Wittmann and Roland Seifert

Trends in Pharmacological Sciences, 2017, 38, 717
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Computational approach towards understanding structural and functional role of cytokinin oxidase/dehydrogenase 2 (CKX2) in enhancing grain yield in rice plant

Gayatri Gouda, Manoj Kumar Gupta, Ravindra Donde, Jitendra Kumar, Ramakrishna Vadde, Trilochan Mohapatra and Lambodar Behera

Journal of Biomolecular Structure and Dynamics, 2020, 38, 1158
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Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex

Jingxiao Zhang, Lilei Zhang, Yangcheng Xu, Shanshan Jiang, Yueyue Shao and Francesca Spyrakis

PLoS ONE, 2018, 13, e0196651
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A general overview on outer membrane protein (Omp) simulations

Yee Siew Choong and Roy Lee Yung-Hung

Journal of Computational Science, 2016, 17, 285
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Descriptive molecular pharmacology of the δ opioid receptor (DOR): A computational study with structural approach

Guillermo Goode-Romero, Laura Dominguez and Sandipan Chakraborty

PLoS ONE, 2024, 19, e0304068
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