Rima D. Alharthy, Ghulam Fatima, Numan Yousaf, Muhammad Shaheen Iqbal, Sadia Sattar, Abdullah R. Alanzi, Ijaz Ali, Muhammad Muddassar and Chandrabose Selvaraj

PLoS ONE, 2023, 18, e0295741
DOI: 10.1371/journal.pone.0295741

Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations

Huayin Bao, Wei Wang, Haibo Sun and Jianzhong Chen

Journal of Enzyme Inhibition and Medicinal Chemistry, 2023, 38
DOI: 10.1080/14756366.2023.2195995

Structural Dynamics of Rho GTPases

Yuan Lin and Yi Zheng

Journal of Molecular Biology, 2025, 437, 168919
DOI: 10.1016/j.jmb.2024.168919

Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins

Angela Parise, Sofia Cresca and Alessandra Magistrato

Expert Opinion on Drug Discovery, 2024, 19, 1259
DOI: 10.1080/17460441.2024.2387856

Mechanism-Based Redesign of GAP to Activate Oncogenic Ras

Dénes Berta, Sascha Gehrke, Kinga Nyíri, Beáta G. Vértessy and Edina Rosta

J. Am. Chem. Soc., 2023, 145, 20302
DOI: 10.1021/jacs.3c04330

Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process

Yuqing Xiong, Juan Zeng, Fei Xia, Qiang Cui, Xianming Deng and Xin Xu

J Comput Chem, 2022, 43, 906
DOI: 10.1002/jcc.26846

Structural insights into non-hotspot KRAS mutations and their potential as targets for effective cancer therapies

Cong Ding, Gaoyuan Wang, Wenqing Zou, Yanping Mao and Jun Ma

Journal of Biomolecular Structure and Dynamics, 2025, 43, 8308
DOI: 10.1080/07391102.2024.2324350

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant

Xiao Liu, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Z. H. Zhang, Zhirong Liu and Zhaoxi Sun

J Comput Aided Mol Des, 2022, 36, 879
DOI: 10.1007/s10822-022-00487-w

Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling

Sian Xiao, Mohammed Alshahrani, Guang Hu, Peng Tao and Gennady Verkhivker

Protein Science, 2025, 34
DOI: 10.1002/pro.70228

Unveiling the State Transition Mechanisms of Ras Proteins through Enhanced Sampling and QM/MM Simulations

Fangchen Hu, Yiqiu Wang, Juan Zeng, Xianming Deng, Fei Xia and Xin Xu

J. Phys. Chem. B, 2024, 128, 1418
DOI: 10.1021/acs.jpcb.3c07666

All-Atom Perspective of the DENV-3 Methyltransferase Inhibition Mechanism

Xiao Liu, Kaiwen Pang, Hangfei Wu, Xiaohui Wang, John Z. H. Zhang and Zhaoxi Sun

J. Phys. Chem. B, 2024, 128, 12358
DOI: 10.1021/acs.jpcb.4c05943

Molecular modelling of ionic liquids: Physical properties of species with extremely long aliphatic chains from a near-optimal regime

Zhaoxi Sun, Abhijit Kayal, Zhihao Gong, Lei Zheng and Qiaole He

Journal of Molecular Liquids, 2022, 367, 120492
DOI: 10.1016/j.molliq.2022.120492

Structure-Based Discovery of Active Pan-KRas Inhibitors Targeting G12D Mutants by Enhanced Sampling Simulations

Juan Zeng, Li Li, Chi Sun, Shen Sheng, Yuhua Tan, Jian Chen, Fei Xia, Xianming Deng and Xin Xu

J. Phys. Chem. B, 2025, 129, 9283
DOI: 10.1021/acs.jpcb.5c01781

Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics

Zhiping Yu, Zhen Wang, Xiuzhen Cui, Zanxia Cao, Wanyunfei Zhang, Kunxiao Sun and Guodong Hu

Molecules, 2024, 29, 645
DOI: 10.3390/molecules29030645

Genetically Encoded Aminocoumarin Lysine for Optical Control of Protein–Nucleotide Interactions in Zebrafish Embryos

Wes Brown, Joshua Wesalo, Subhas Samanta, Ji Luo, Steven E. Caldwell, Michael Tsang and Alexander Deiters

ACS Chem. Biol., 2023, 18, 1305
DOI: 10.1021/acschembio.3c00028

GTP-Bound N-Ras Conformational States and Substates Are Modulated by Membrane and Point Mutation

Alexandra Farcas and Lorant Janosi

IJMS, 2024, 25, 1430
DOI: 10.3390/ijms25031430

Expanding the Genetic Code of Xenopus laevis Embryos

Wes Brown, Lance A. Davidson and Alexander Deiters

ACS Chem. Biol., 2024, 19, 516
DOI: 10.1021/acschembio.3c00686

Mutations influence the conformational dynamics of the GDP/KRAS complex

Congcong Shen, Jie Yin, Min Wang, Zhiping Yu, Xin Xu, Zhongshun Zhou, Yingshi Hu, Caijuan Xia and Guodong Hu

Journal of Biomolecular Structure and Dynamics, 2025, 43, 10384
DOI: 10.1080/07391102.2024.2331627

Deciphering Selectivity Mechanism of BRD9 and TAF1(2) toward Inhibitors Based on Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations

Lifei Wang, Yan Wang, Yingxia Yu, Dong Liu, Juan Zhao and Lulu Zhang

Molecules, 2023, 28, 2583
DOI: 10.3390/molecules28062583

Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics Simulations

Shuhua Shi, Linqi Zheng, Yonglian Ren and Ziyu Wang

Molecules, 2023, 28, 2886
DOI: 10.3390/molecules28072886

Molecular modelling of ionic liquids: Perfluorinated anionic species with enlarged halogen substitutions

Zhaoxi Sun, Lei Zheng, Zuo-yuan Zhang, Yalong Cong, Jingjing Yang and Xiaohui Wang

Journal of Molecular Liquids, 2023, 378, 121599
DOI: 10.1016/j.molliq.2023.121599

Engineering Small Molecule Switches of Protein Function in Zebrafish Embryos

Wes Brown, Joshua Wesalo, Michael Tsang and Alexander Deiters

J. Am. Chem. Soc., 2023, 145, 2395
DOI: 10.1021/jacs.2c11366

Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning

Jianzhong Chen, Jian Wang, Wanchun Yang, Lu Zhao and Guodong Hu

J. Chem. Inf. Model., 2024, 64, 6880
DOI: 10.1021/acs.jcim.4c01174