Integrated discovery of FOXO1–DNA stabilizers from marine natural products to restore chemosensitivity to anti-EGFR-based therapy for metastatic lung cancer

Yingjia Sun, Xinghao Ai, Jingwen Hou, Xiangyun Ye, Ruijun Liu, Shengping Shen, Ziming Li and Shun Lu

Molecular BioSystems, 2016, 13, 330
DOI: 10.1039/C6MB00678G

Is protein context responsible for peptide-mediated interactions?

Peng Zhou, Qingqing Miao, Fugang Yan, Zhongyan Li, Qianhu Jiang, Li Wen and Yang Meng

Molecular Omics, 2019, 15, 280
DOI: 10.1039/C9MO00041K

Context contribution to the intermolecular recognition of human ACE2-derived peptides by SARS-CoV-2 spike protein: implications for improving the peptide affinity but not altering the peptide specificity by optimizing indirect readout

Peng Zhou, Heyi Wang, Zheng Chen and Qian Liu

Molecular Omics, 2020, 17, 86
DOI: 10.1039/D0MO00103A

Molecular insight into mutation-induced conformational change in metastasic bowel cancer BRAF kinase domain and its implications for selective inhibitor design

Kai Zhao, Xin Zhou and Ming Ding

Journal of Molecular Graphics and Modelling, 2018, 79, 59
DOI: 10.1016/j.jmgm.2017.11.005

Rational Design and Intramolecular Cyclization of Hotspot Peptide Segments at YAP–TEAD4 Complex Interface

Dingwa Zhang, Deyong He, Xiaoliang Pan and Lijun Liu

PPL, 2020, 27, 999
DOI: 10.2174/0929866527666200414160723

Exploring the systematic effect of N‐substituted PxxP motifs on peptoid affinity to ARHGEF5/TIM SH3 domain and its relationship with ARHGEF5/TIM activation

Yong Fu, Ping He, Yu Zhou, Shengyuan Huang, Lin Liang and Shengchun Liu

Proteins, 2019, 87, 979
DOI: 10.1002/prot.25760

Targeting Self-Binding Peptides as a Novel Strategy To Regulate Protein Activity and Function: A Case Study on the Proto-oncogene Tyrosine Protein Kinase c-Src

Zhengya Bai, Shasha Hou, Shilei Zhang, Zhongyan Li and Peng Zhou

J. Chem. Inf. Model., 2017, 57, 835
DOI: 10.1021/acs.jcim.6b00673

Rational design and improvement of the dimerization‐disrupting peptide selectivity between ROCK‐I and ROCK‐II kinase isoforms in cerebrovascular diseases

Zhengtian Gu, Tingting Yan and Fuling Yan

J of Molecular Recognition, 2020, 33
DOI: 10.1002/jmr.2835

Rational truncation, mutation, and halogenation of bradykinin neuropeptides as potent ACEII inhibitors by integrating molecular dynamics simulations, quantum mechanics calculations, and in vitro assays

Jun Fu, Shenghui Chen and Zhong Ni

J Chinese Chemical Soc, 2022, 69, 1569
DOI: 10.1002/jccs.202200242

Systematic profiling of staralog response to acquired drug resistant kinase gatekeeper mutations in targeted cancer therapy

Yuping Yang, Yue Qiu, Xu Liu, Yanhua Liu, Yaling Yin and Peng Li

Amino Acids, 2020, 52, 511
DOI: 10.1007/s00726-020-02832-5

Integrated Computational/Experimental Identification, Phosphorylation and Stapling of an Intramolecular Auto-Inhibitory Helical Segment C-Terminal to Breast Cancer Her2 Kinase Domain

Min Dong and Weiwei Huang

J. Comput. Biophys. Chem., 2025, 24, 1403
DOI: 10.1142/S2737416525500292

Conversion of MIG6 peptide from the nonbinder to binder of lung cancer-related EGFR by phosphorylation and cyclization

Na Li and Meng Wei

Artificial Cells, Nanomedicine, and Biotechnology, 2017, 45, 1023
DOI: 10.1080/21691401.2016.1200058

Rational Optimization of Tumor Suppressor‐Derived Peptide Inhibitor Selectivity between Oncogene Tyrosine Kinases ErbB1 and ErbB2

Yilin Deng and Jian Li

Archiv der Pharmazie, 2017, 350
DOI: 10.1002/ardp.201700181

Rational design of stapled helical peptides as antidiabetic PPARγ antagonists to target coactivator site by decreasing unfavorable entropy penalty instead of increasing favorable enthalpy contribution

Yang Zhang, Jie Wang, Wenchao Li and Ying Guo

Eur Biophys J, 2022, 51, 535
DOI: 10.1007/s00249-022-01616-x

Conformational stabilization of FOX–DNA complex architecture to sensitize prostate cancer chemotherapy

Bin Chen, Huiqiang Wang, Zhun Wu, Bo Duan, Peide Bai, Kaiyan Zhang, Wei Li, Jiaxin Zheng and Jinchun Xing

Amino Acids, 2017, 49, 1247
DOI: 10.1007/s00726-017-2426-1

Revisiting the structural basis and energetic landscape of susceptibility difference between HLA isotypes to allergic rhinitis

Xin-Li Mao, Feng Zhu, Zhao-Hu Pan, Guo-Min Wu and Hong-Yuan Zhu

Computational Biology and Chemistry, 2016, 64, 210
DOI: 10.1016/j.compbiolchem.2016.07.001

Integrated in silico–in vitro screening of ovarian cancer peroxisome proliferator-activated receptor-γ agonists against a biogenic compound library

Gui-Lian Zhang, Feng-Ying Liu, Jing Zhang, Li-Ping Wang, Er-Xia Jia and Shi-Ming Lv

Med Chem Res, 2018, 27, 341
DOI: 10.1007/s00044-017-2060-1

Molecular mechanism of D816X mutation-induced c-Kit activation and -mediated inhibitor resistance in gastrointestinal stromal tumor

Haohai Jiang, Weiwei Shao, Yuanjin Wang, Ronghui Xu, Linsen Zhou and Xiangming Mu

Journal of Molecular Graphics and Modelling, 2018, 84, 189
DOI: 10.1016/j.jmgm.2018.07.003

Electrostatic explanation of D1228V/H/N-induced c-Met resistance and sensitivity to type I and type II kinase inhibitors in targeted gastric cancer therapy

Zhen Xu, Pingping Hu, Dong Fang, Lingna Ni and Jianzhong Xu

J Mol Model, 2019, 25
DOI: 10.1007/s00894-018-3893-3

Rational molecular targeting of the inter-subunit interaction between human cardiac troponin hcTnC and hcTnI using switch peptide-competitive biogenic medicines

Danrui Xiao, Zixun Fan, Wu Jiaqi, Hua Liu, Linghong Shen, Ben He and Min Zhang

Computational Biology and Chemistry, 2020, 87, 107272
DOI: 10.1016/j.compbiolchem.2020.107272

Molecular design and engineering of phosphopeptide ligands to target lung cancer polo-like kinase

Xiyan Yu, Yanwen Li, Ying Lou and Tong Wang

Biotechnol Bioproc E, 2017, 22, 218
DOI: 10.1007/s12257-016-0441-9

Rational Design and Cyclization of MIG6 Peptide to Restore its Binding Affinity for ErbB Family Receptor Tyrosine Kinases

Dingwa Zhang, Deyong He, Ling Huang, Yaping Xu and Lijun Liu

Int J Pept Res Ther, 2018, 24, 71
DOI: 10.1007/s10989-017-9593-5

Machine learning-guided evolution of BMP-2 knuckle Epitope-Derived osteogenic peptides to target BMP receptor II

Wei Zhang, Jiazhi Liu, Haojie Shan, Fuli Yin, Biao Zhong, Chi Zhang and Xiaowei Yu

Journal of Drug Targeting, 2020, 28, 802
DOI: 10.1080/1061186X.2020.1757100

Exploring calcium ion-dependent effect on the intermolecular interaction between human secreted phospholipase A2 and its peptide inhibitors in coronary artery disease

Guanggan Bo, Fang Cao, Min Li, Junwu Xing, Xiaoye Su, Yunxian Zhu and Dingkun Wu

Journal of Molecular Graphics and Modelling, 2019, 93, 107449
DOI: 10.1016/j.jmgm.2019.107449

Structure-based design and disulfide stapling of interfacial cyclic peptidic inhibitors from thymic stromal lymphopoietin (TSLP) receptor to competitively target TSLP

Quan He, Guangfei Wei, Xiaomei Ma, Weiqi Feng, Xuzhi Lu and Zhongxing Li

Biochimie, 2025, 230, 156
DOI: 10.1016/j.biochi.2024.11.012

Molecular design of Stat3‐derived peptide selectivity between BET proteins Brd2 and Brd4 in ovarian cancer

Lixia Zhu and Xi Ding

J of Molecular Recognition, 2018, 31
DOI: 10.1002/jmr.2679

Design and verification of halogen-bonding system at the complex interface of human fertilization-related MUP PDZ5 domain with CAMK’s C-terminal peptide

Juan Wang, Yunjie Guo and Xue Zhang

Computational Biology and Chemistry, 2018, 72, 164
DOI: 10.1016/j.compbiolchem.2017.11.007

Computational design of peptide ligands to target the intermolecular interaction between viral envelope protein and pediatric receptor

Darong Xu, Hongliang Bian, Jinlan Cai, Daocheng Bao, Qing Jin, Min Zhu, Cuifeng Zhang and Tingting Tao

Computational Biology and Chemistry, 2017, 69, 120
DOI: 10.1016/j.compbiolchem.2017.06.001

Rational molecular design of novel class-III peptidic antagonists to competitively disrupt human PPARδ self-binding peptide

Yue Peng, Zilong Li, Yunyi Zhang, Haiyang Ye, Li Mei, Shuyong Shang and Peng Zhou

J Comput Aided Mol Des, 2025, 39
DOI: 10.1007/s10822-025-00594-4

Rational creation and systematic analysis of cervical cancer kinase–inhibitor binding profile

Min Han and Dongdong Sun

J Comput Aided Mol Des, 2019, 33, 689
DOI: 10.1007/s10822-019-00211-1

Systematic identification of the druggable interactions between human protein kinases and naturally occurring compounds in endometriosis

Lai Jiang, Chaoliang Tang, Jie Rao, Qing Xue, Hao Wu, Dabao Wu, Aijun Zhang, Ling Chen, Zhen Shen and Lei Lei

Computational Biology and Chemistry, 2017, 71, 136
DOI: 10.1016/j.compbiolchem.2017.10.006

Identification and characterization of the druggable kinase targets of olmesartan and its analogues from a systematic kinase–chemical interaction profile in atherosclerosis

Rui-Juan Zhuang, Wei-Dong Jin, Xiao-Yan Wang and Xue-Ming Wu

Journal of Molecular Graphics and Modelling, 2018, 80, 211
DOI: 10.1016/j.jmgm.2018.01.016

Targeting oncogenic transcriptional corepressor Nac1 POZ domain with conformationally constrained peptides by cyclization and stapling

Tao Wu, Ping He, Wei Wu, Yingli Chen and Fenglin Lv

Bioorganic Chemistry, 2018, 80, 1
DOI: 10.1016/j.bioorg.2018.05.024

Peptide Scaffold-Based Discovery of Nonpeptide Natural Medicines to Target PI3K p85 SH2 Domain

Chong Xu, Jing Leng, Chuncao Wu, Min Yang, Quan Sun and Dan Song

Int J Pept Res Ther, 2018, 24, 61
DOI: 10.1007/s10989-017-9591-7

Molecular modeling and chemometric analysis of osteoporosis calmodulin‐TRPV1 binding affinity by statistically characterizing complex interactions

Xudong Liu, Limin Zhu, Lei Wang, Lingzhi Yu and Cong Gao

Journal of Chemometrics, 2018, 32
DOI: 10.1002/cem.2989

Why the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate Src homology 3 domain in class II mode?

Peng Zhou, Fugang Yan, Qingqing Miao, Zheng Chen and Heyi Wang

Journal of Biomolecular Structure and Dynamics, 2021, 39, 310
DOI: 10.1080/07391102.2019.1709547

Systematic analysis and identification of unexpected interactions from the neuroprotein drug interactome in hydrocephalus pharmacological intervention

Youming Lu, Lei Yuan, Xin Chen, Aijun Zhang, Pengqi Zhang and Dongdong Zou

J. Bioinform. Comput. Biol., 2019, 17, 1950002
DOI: 10.1142/S0219720019500021

Molecular dynamics directed rational design and fluorescence binding assay of phosphopeptide ligands for PLK polo-box domain

Deyong He, Ling Huang, Yaping Xu, Xiaoliang Pan and Lijun Liu

Molecular Simulation, 2017, 43, 176
DOI: 10.1080/08927022.2016.1244605

Systematic analysis and integrative discovery of active-site subpocket-specific dehydroquinate synthase inhibitors combating antibiotic-resistant Staphylococcus aureus infection

Quanfeng Liu, Liping Li and Fei Xu

J. Bioinform. Comput. Biol., 2018, 16, 1850027
DOI: 10.1142/S0219720018500270

Comprehensive evaluation and systematic comparison of Gaussian process (GP) modelling applications in peptide quantitative structure-activity relationship

Haiyang Ye, Yunyi Zhang, Zilong Li, Yue Peng and Peng Zhou

Chemometrics and Intelligent Laboratory Systems, 2024, 252, 105191
DOI: 10.1016/j.chemolab.2024.105191

Rational design and exploitation of the molecular diversity space of PRX1‐derived SRX1 peptidic inhibitors containing proteinogenic and nonproteinogenic amino acids

Haijin Yang, Ping Li, Yanxin Wan, Rongyuan Qiu, Mengxi Xiao, Zhiyuan Zhu and Xiaoqiong Wu

J Chinese Chemical Soc, 2025, 72, 427
DOI: 10.1002/jccs.70001

Structure-Based Optimization of Therapeutic Peptide Selectivity Between Cerebrovascular Rho-1 and Rho-2 Kinase Isoforms

Zhengtian Gu, Tingting Yan and Fuling Yan

Int J Pept Res Ther, 2020, 26, 2419
DOI: 10.1007/s10989-020-10032-8

Peptide selectivity between the PDZ domains of human pregnancy‐related serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) can be reshaped by different halogen probes

Mei‐Ling Sun, Li‐Mei Sun and Yong‐Qing Wang

J of Molecular Recognition, 2018, 31
DOI: 10.1002/jmr.2698

Molecular modeling and rational design of hydrocarbon-stapled/halogenated helical peptides targeting CETP self-binding site: Therapeutic implication for atherosclerosis

Jian Zhu, Sen Wei, Linchen Huang, Qi Zhao, Haichao Zhu and Anwei Zhang

Journal of Molecular Graphics and Modelling, 2020, 94, 107455
DOI: 10.1016/j.jmgm.2019.107455

Systematic response of staurosporine scaffold‐based inhibitors to drug‐resistant cancer kinase mutations

Yongkang He

Archiv der Pharmazie, 2020, 353
DOI: 10.1002/ardp.201900320

Grafting, Stripping and Stapling of Helical Peptides from the Dimerization Interface of ONFH-Related Bone Morphogenetic Protein-2

Wenqi Song, Kunzheng Wang, Wei Wang, Pei Yang and Xiaoqian Dang

Protein J, 2019, 38, 12
DOI: 10.1007/s10930-018-9807-5

Systematic profiling of clinical missence mutation effects on the intermolecular interaction between human growth hormone and its receptor in isolated growth hormone deficiency

Hui Liu, Liangpu Xu, Hailong Huang, Peiran Zhao, Rongrong Yang, Qing Zhou and Guanghua Liu

Journal of Molecular Graphics and Modelling, 2019, 92, 1
DOI: 10.1016/j.jmgm.2019.06.018

Disrupting the intramolecular interaction between proto-oncogenec-Src SH3 domain and its self-binding peptide PPII with rationally designed peptide ligands

Peng Zhou, Shasha Hou, Zhengya Bai, Zhongyan Li, Heyi Wang, Zheng Chen and Yang Meng

Artificial Cells, Nanomedicine, and Biotechnology, 2018, 46, 1122
DOI: 10.1080/21691401.2017.1360327

Electrostatic mechanism of V600E mutation-induced B-Raf constitutive activation in colorectal cancer: molecular implications for the selectivity difference between type-I and type-II inhibitors

Tie Liu, Zhaoshun Wang, Peng Guo and Na Ding

Eur Biophys J, 2019, 48, 73
DOI: 10.1007/s00249-018-1334-y

Rational Derivation of Osteogenic Peptides from Bone Morphogenetic Protein-2 Knuckle Epitope by Integrating In Silico Analysis and In Vitro Assay

Aiying Zhang, Zhixia Chen, Xiuli Yu, Li Zhang and Qiyuan Song

Int J Pept Res Ther, 2021, 27, 25
DOI: 10.1007/s10989-020-10058-y

Structural modeling of osteoarthritis ADAMTS4 complex with its cognate inhibitory protein TIMP3 and rational derivation of cyclic peptide inhibitors from the complex interface to target ADAMTS4

Wei Zhang, Biao Zhong, Chi Zhang, Yukai Wang, Shang Guo, Congfeng Luo and Yulin Zhan

Bioorganic Chemistry, 2018, 76, 13
DOI: 10.1016/j.bioorg.2017.10.017

Disruption of the intramolecular interaction between human lung cancer-related EGFR kinase domain and carboxy-terminal tail by intra-Tyr1016 phosphorylation or extra-peptidic competitors

Tian-Chang Zhen, Yan Wu and Xian-Qi Zhang

J Mol Model, 2026, 32
DOI: 10.1007/s00894-026-06635-5

Computational redesign of human respiratory syncytial virus epitope as therapeutic peptide vaccines against pediatric pneumonia

Xiangxiang Shi, Jun Zheng and Tingting Yan

J Mol Model, 2018, 24
DOI: 10.1007/s00894-018-3613-z

Structural Identification and Systematic Comparison of Phorbol Ester, Dioleoylglycerol, Alcohol and Sevoflurane Binding Sites in PKCδ C1A Domain

Lijie Shi

Protein J, 2018, 37, 539
DOI: 10.1007/s10930-018-9793-7

Theoretical insights into the binding of mono/di-ethyl phthalates to superoxide dismutase and associated structural changes impairing antioxidant activity: A coupled molecular docking and dynamics simulation approach

Xiuli Fan, Chenggang Gu, Lezu Shen, Zhengyuan Gao, Xinglun Yang, Yongrong Bian, Fang Wang and Xin Jiang

Science of The Total Environment, 2025, 983, 179667
DOI: 10.1016/j.scitotenv.2025.179667

Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling

Peng Zhou, Qian Liu, Ting Wu, Qingqing Miao, Shuyong Shang, Heyi Wang, Zheng Chen, Shaozhou Wang and Heyan Wang

J. Chem. Inf. Model., 2021, 61, 1718
DOI: 10.1021/acs.jcim.0c01370

Statistical analysis and heuristic identification of unexpected interactions from the neurokinase‐inhibitor interactome in trigeminal neuralgia pharmacological intervention

Lei Liu, Xiaobing Chen, Weiju Liu, Hui Yu and Fangming Liu

Journal of Chemometrics, 2019, 33
DOI: 10.1002/cem.3126

EGFR affinity and selectivity for the phosphorylation codes of pseudo triad tyrosine (YYY) motif and its extensions in lung cancer-related substrate-inhibitor alignment: an integrated molecular simulation-QSAR modelling–in vitro assay approach

Z. Wang, L. Dong, H. Liu and Y. Song

SAR and QSAR in Environmental Research, 2025, 36, 1263
DOI: 10.1080/1062936X.2025.2599971

Systematic characterization of adenosine triphosphate response to lung cancer epidermal growth factor receptor missense mutations: A molecular insight into “generic” drug resistance mutations

Hui Wang, Zengjian Yang and Yanliang Liu

J Chinese Chemical Soc, 2020, 67, 1903
DOI: 10.1002/jccs.201900435

Statistical molecular identification of kinase inhibitors to disrupt c‐Jun N‐terminal protein kinase involved in paraquat‐mediated toxicological effects

Yu‐Ping Yang, Yu‐Mei Jin and Zhi‐Yuan Zhu

Journal of Chemometrics, 2017, 31
DOI: 10.1002/cem.2905

Hydrocarbon-stapling stabilization of the reduced homodimerization interaction of hepatic cancer DAP12 transmembrane domain in water phase

Wenqing Tang, Chen Wang, Yingting Zhou, Jing Luo, Tao Ye and Biwei Yang

Chem. Pap., 2020, 74, 2153
DOI: 10.1007/s11696-019-01016-0

Genome-wide Analysis, Computational Modeling and Competition Assay of the Intermolecular Interaction Profile Between Human SH2-ome and the Putative Phosphorylation Sites of PDGFRA C-terminal Tail

Dandan Liu, Qiping Luo, Daofa Tian and Bin Xiao

J. Comput. Biophys. Chem., 2026, 25, 2293
DOI: 10.1142/S2737416526500109

Directed Molecular Engineering of Mig6 Peptide Selectivity between Proto-oncogene ErbB Family Receptor Tyrosine Kinases

Zhijun Qiao and Shuai Wang

Biotechnol Bioproc E, 2021, 26, 277
DOI: 10.1007/s12257-020-0102-x

Molecular design of sequence‐minimized, structure‐optimized, and hydrocarbon‐stapled helix–helix interactions in the trimer‐of‐hairpins motif of pediatric pneumonia RSV‐F protein

Jihong Wang, Jingxiu Zhang, Xiangguo Sun, Chengjun Liu, Xingli Li and Lei Chen

Chem Biol Drug Des, 2019, 94, 1292
DOI: 10.1111/cbdd.13501

Self-binding peptides: Binding-upon-folding versus folding-upon-binding

Zhongyan Li, Fugang Yan, Qingqing Miao, Yang Meng, Li Wen, Qianhu Jiang and Peng Zhou

Journal of Theoretical Biology, 2019, 469, 25
DOI: 10.1016/j.jtbi.2019.02.014

Rational derivation of CETP self-binding helical peptides by π-π stacking and halogen bonding: Therapeutic implication for atherosclerosis

Jian Zhu, Meijuan Lu and Lixia Zhu

Bioorganic Chemistry, 2016, 68, 259
DOI: 10.1016/j.bioorg.2016.08.012

TAZ‐hTrap: A Rationally Designed, Disulfide‐Stapled Tead Helical Hairpin Trap to Selectively Capture Hippo Signaling Taz With Potent Antigynecological Tumor Activity

Bin Tang, Yu Du and Jun Wang

J of Molecular Recognition, 2025, 38
DOI: 10.1002/jmr.3111

Structural analysis and rational design of orthogonal stacking system in an E. coli DegP PDZ1–peptide complex

Dingwa Zhang, Deyong He, Xiaoliang Pan, Yaping Xu and Lijun Liu

Chem. Pap., 2019, 73, 2469
DOI: 10.1007/s11696-019-00797-8

Rational design of EGFR dimerization-disrupting peptides: A new strategy to combat drug resistance in targeted lung cancer therapy

Qiuhong Liu, Jinqiao Zhou, Jing Gao, Wentao Ma, Shilei Wang and Lihua Xing

Biochimie, 2020, 176, 128
DOI: 10.1016/j.biochi.2020.07.010

Inverse in silico–in vitro fishing of unexpected paroxetine kinase targets from tumor druggable kinome

Weiyan Zhou, Hongbo Yang and Haifeng Wang

J Mol Model, 2020, 26
DOI: 10.1007/s00894-020-04444-y

Rational Design and Protein Engineering of {SH2 Domain–≫ Flexible Linker–≫ Self‐Controlling Peptide} Fusion System With Phosphorylation‐Regulated Molecular Switch Functionality

Peng Zhou, Yunyi Zhang, Kexin Li, Haiyang Ye, Li Mei and Shuyong Shang

Biotech & Bioengineering, 2025, 122, 2511
DOI: 10.1002/bit.29044

Computational design and experimental confirmation of a disulfide-stapled YAP helixα1-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity

Kaipeng Li and Lijun Liu

J Comput Aided Mol Des, 2024, 38
DOI: 10.1007/s10822-024-00572-2

Systematic Profiling and Evaluation of Structure-based Kinase–Inhibitor Interactome in Cervical Cancer by Integrating In Silico Analyses and In Vitro Assays at Molecular and Cellular Levels

Li-Xia Zhu, Qin Liu, Ya-Fang Hua, Ning Yang, Xue-Gang Zhang and Xi Ding

Computational Biology and Chemistry, 2019, 80, 324
DOI: 10.1016/j.compbiolchem.2019.04.016

Targeting the membrane fusion event of human respiratory syncytial virus with rationally designed α-helical hairpin traps

Qiuhong Liu, Jinqiao Zhou, Jing Gao, Xiaoqin Zhang, Jingrui Yang, Chunling Hu, Weili Chu and Mengying Yao

Life Sciences, 2021, 280, 119695
DOI: 10.1016/j.lfs.2021.119695

Genome-wide analysis of LXXLL-mediated DAX1/SHP–nuclear receptor interaction network and rational design of stapled LXXLL-based peptides to target the specific network profile

Haihong Qian, Ping He, Fenglin Lv and Wei Wu

International Journal of Biological Macromolecules, 2019, 129, 13
DOI: 10.1016/j.ijbiomac.2019.02.014

Structure‐based statistical modeling and analysis of peptide affinity and cross‐reactivity to human senile osteoporosis OSF SH3 domain

Wei Zhang, Biao Zhong, Yulin Zhan and Congfeng Luo

Journal of Chemometrics, 2018, 32
DOI: 10.1002/cem.2967

Structure-based derivation and intramolecular cyclization of peptide inhibitors from PD-1/PD-L1 complex interface as immune checkpoint blockade for breast cancer immunotherapy

Kun Zhou, Ji Lu, Xiaoxin Yin, Han Xu, Longzhi Li and Baojin Ma

Biophysical Chemistry, 2019, 253, 106213
DOI: 10.1016/j.bpc.2019.106213

Inverse screening of Simvastatin kinase targets from glioblastoma druggable kinome

Yi Li, Xu Wei, Qiuhong Wang, Wei Li and Tao Yang

Computational Biology and Chemistry, 2020, 86, 107243
DOI: 10.1016/j.compbiolchem.2020.107243

Integration of virtual screening and susceptibility test to discover active-site subpocket-specific biogenic inhibitors of Helicobacter pylori shikimate dehydrogenase

Kuifeng Wang, Min Zhu, Yongzhi Tang, Junyan Liu, Fei Yan, Zhenjun Yu and Jiansheng Zhu

Int Microbiol, 2019, 22, 69
DOI: 10.1007/s10123-018-0029-7

Rational design of potent phosphopeptide binders to endocrine Snk PBD domain by integrating machine learning optimization, molecular dynamics simulation, binding energetics rescoring, and in vitro affinity assay

Zhaohui Wang, Jixiao Lan, Yan Feng, Yumei Chen and Meiyuan Chen

Eur Biophys J, 2025, 54, 33
DOI: 10.1007/s00249-024-01729-5

Systematic Identification and Comparative Analysis of Human Cartilage-Derived Self-peptides Presented Differently by Ankylosing Spondylitis (AS)-Associated HLA-B*27:05 and Non-AS-associated HLA-B*27:09

Chang Ge, Wenzhi Zhang, Rui He and Haiping Cai

Int J Pept Res Ther, 2020, 26, 513
DOI: 10.1007/s10989-019-09857-9

Structure-based design of competitive ligands to target Spon2 in gastric cancer: An integration of molecular modeling and in vitro assay

Zhenglei Xu, Zhichao Yu, Shumei Nai, Ruiyue Shi, Qinhong Tang, Haiyang Zhang, Lijuan Ye, Lisheng Wang and Yincai Hong

Bioorganic Chemistry, 2017, 74, 115
DOI: 10.1016/j.bioorg.2017.07.011

Systematic profiling of SH3-mediated Tau–Partner interaction network in Alzheimer's disease by integrating in silico analysis and in vitro assay

Xiaoming Wang, Chunyan Chang, Dongxue Wang and Shanchao Hong

Journal of Molecular Graphics and Modelling, 2019, 90, 265
DOI: 10.1016/j.jmgm.2019.05.004

Computational Analysis and Rational Design of N-Substituting Perturbation on the Affinity and Specificity of Pediatric Fyn SH3–Peptoid Interaction

Qin Liu, Jie Wang, Lin Shi and Xiang Shao

J. Comput. Biophys. Chem., 2023, 22, 765
DOI: 10.1142/S2737416523500394

Molecular selectivity design of mitogen-inducible gene-derived phosphopeptides between oncogenic HER kinases

Xiuli Yu, Aiying Zhang, Guoyu Sun and Xuebo Li

Journal of Molecular Graphics and Modelling, 2020, 99, 107661
DOI: 10.1016/j.jmgm.2020.107661

Studying Calcium Ion-Dependent Effect on the Inter-subunit Interaction Between the cTnC N-terminal Domain and cTnI C-terminal Switch Peptide of Human Cardiac Troponin via Chou’s 5-Steps Rule

Wenmin Yu, Yuan Lv, Yingpeng Ding and Shu Ding

Int J Pept Res Ther, 2020, 26, 675
DOI: 10.1007/s10989-019-09875-7

Interleukin‐1α, interleukin‐1β and interleukin‐1 receptor antagonist share a common U‐shaped recognition epitope on interleukin‐1 receptor surface

Huaijun Ma, Jie Liu, Wei Wu and Ping He

J of Molecular Recognition, 2022, 35
DOI: 10.1002/jmr.2963

Competitive Disruption of the Intermolecular Interaction Between Anesthetic PKC Isozyme ζ and its Cognate Substrates using Halogenated Peptidic Inhibitors with Affinity Improved by a Designer Halogen(X)/Hydrogen(H)-Bonding (dgr[XHB]) System

Fang Lian, Zhong Wang, Zhidong Zhou and Xiaohong Du

Int J Pept Res Ther, 2025, 31
DOI: 10.1007/s10989-025-10704-3

Structure-based rational design of self-inhibitory peptides to disrupt the intermolecular interaction between the troponin subunits C and I in neuropathic pain

Junmin Yu, Shilei Wang, Junjie Yu, Chuansheng Liu, Fenghe Xu, Shijie Wang, Yusheng Yi and Yanwei Yin

Bioorganic Chemistry, 2017, 73, 10
DOI: 10.1016/j.bioorg.2017.05.004

Molecular design and optimization of hepatic cancer SLP76‐derived PLCγ1 SH3‐binding peptide with the systematic N‐substitution of peptide PXXP motif

Wenqing Tang, Zhiying Zhao, Chen Wang, Tao Ye and Biwei Yang

J of Molecular Recognition, 2019, 32
DOI: 10.1002/jmr.2806

The C‐terminal self‐binding helical peptide of human estrogen‐related receptor γ can be druggably targeted by a novel class of rationally designed peptidic antagonists

Zilong Li, Yue Peng, Haiyang Ye, Yunyi Zhang and Peng Zhou

J Comput Chem, 2024, 45, 2771
DOI: 10.1002/jcc.27473

Computational modeling of cyclic peptide inhibitor–MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations

Yeng-Tseng Wang and Tian-Lu Cheng

Journal of Biomolecular Structure and Dynamics, 2021, 39, 4005
DOI: 10.1080/07391102.2020.1773317

Current Computational Methods for Protein-peptide Complex Structure Prediction

Chao Yang, Xianjin Xu and Changcheng Xiang

CMC, 2024, 31, 4058
DOI: 10.2174/0109298673263447230920151524

Molecular insight into the T798M gatekeeper mutation-caused acquired resistance to tyrosine kinase inhibitors in ErbB2-positive breast cancer

Ji Lu, Kun Zhou, Xiaoxing Yin, Han Xu and Baojin Ma

Computational Biology and Chemistry, 2019, 78, 290
DOI: 10.1016/j.compbiolchem.2018.12.007

Rational discovery of novel type-III FTF antagonists to competitively suppress TIF-2 coactivation in liver cancer

Linlin Xu, Zhongming Chen, Keke Shao, Yungang Wang, Leilei Cui and Naizhou Guo

Journal of Receptors and Signal Transduction, 2019, 39, 304
DOI: 10.1080/10799893.2019.1690513

Systematic profiling of substrate binding response to multidrug-resistant mutations in HIV-1 protease: Implication for combating drug resistance

Yonglei Lv, Jianbing Li, Jianhua Fang, Xiufeng Jiao, Lumin Yan and Baifeng Shan

Journal of Molecular Graphics and Modelling, 2017, 74, 83
DOI: 10.1016/j.jmgm.2017.03.009

Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia

Xiaolu Bai and Xiaolin Chen

Journal of Theoretical Biology, 2019, 473, 44
DOI: 10.1016/j.jtbi.2019.03.018

De Novo Hydrocarbon-Stapling Design of Single-Turn α-Helical Antimicrobial Peptides

Zhixia Chen, Xiuli Yu, Aiying Zhang, Fangfang Wang and Yankun Xing

Int J Pept Res Ther, 2020, 26, 1711
DOI: 10.1007/s10989-019-09964-7

Identification of small-molecule ligands that bind to MiR-21 as potential therapeutics for endometriosis by screening ZINC database and in-vitro assays

Songping Liu, Yuxing Yang, Wei Li, Xin Tian, Hongyan Cui and Qiong Zhang

Gene, 2018, 662, 46
DOI: 10.1016/j.gene.2018.03.094

Computational analysis and protein engineering of artificial PDZ domain/self-binding peptide fusion biomacromolecular system with molecular switch functionality

Peng Zhou, Yunyi Zhang, Kexin Li, Haiyang Ye, Li Mei and Shuyong Shang

International Journal of Biological Macromolecules, 2025, 308, 142432
DOI: 10.1016/j.ijbiomac.2025.142432

Computational systematic selectivity of the Fasalog inhibitors between ROCK-I and ROCK-II kinase isoforms in Alzheimer’s disease

Laijun Song, Chunyu Zhu, Wenxin Zheng, Dan Lu, Hong Jiao, Rongbing Zhao and Zhonglei Bao

Computational Biology and Chemistry, 2020, 87, 107314
DOI: 10.1016/j.compbiolchem.2020.107314

Novel Antibacterial Targets in Protein Biogenesis Pathways

Upasana S. Potteth, Tulsi Upadhyay, Snehlata Saini and Ishu Saraogi

ChemBioChem, 2022, 23
DOI: 10.1002/cbic.202100459

Systematic molecular profiling of non-native N6-substitution effects on m6A binding to the YTH domains of human RNA m6A readers in diabetes

Yuting Li, Peng Tan, Qianpan Liu, Huaixin Sun, Yue Wang, Siyi Chen, Weixin Kong, Xiaoyi Sun and Xiang Shao

Biophysical Chemistry, 2025, 320-321, 107417
DOI: 10.1016/j.bpc.2025.107417

In silico-in vitro discovery of untargeted kinase–inhibitor interactions from kinase-targeted therapies: A case study on the cancer MAPK signaling pathway

Li Meng and Zhijun Huang

Computational Biology and Chemistry, 2018, 75, 196
DOI: 10.1016/j.compbiolchem.2018.05.012

Revisiting the molecular mechanism of acquired resistance to reversible tyrosine kinase inhibitors caused by EGFR gatekeeper T790M mutation in non-small-cell lung cancer

Yan Zhao, Yingjie Jiao, Fengzhe Sun and Xudong Liu

Med Chem Res, 2018, 27, 2160
DOI: 10.1007/s00044-018-2224-7

Structural Dissection and Optimization of a Cation–π–π Stacking System in Human Pregnancy-Related Serine Protease–Peptide Complex

Qing-Li Wen, Juan Wang and Yun-Jie Guo

Int J Pept Res Ther, 2020, 26, 589
DOI: 10.1007/s10989-019-09866-8

Structure-based identification, phosphorylation, cyclization and engineering of a self-binding peptide carboxy-terminal to EGFR kinase domain by integrating dynamics simulation, energetics calculation and fluorescence analysis

Jingjing Chen, Tianyu Wang and Lijuan Shi

Eur Biophys J, 2026
DOI: 10.1007/s00249-026-01823-w

Identification, characterization, and comparison of n-alkanols and anesthetics binding to the C1b subdomain of protein kinase cα: similar function with different binding sites

Fang Lian, Zhong Wang, Zhidong Zhou and Guohai Xu

Journal of Receptors and Signal Transduction, 2020, 40, 109
DOI: 10.1080/10799893.2020.1726950

Fishing wild-type sparing inhibitors of proto-oncogene c-met variants in renal cell carcinoma from a curated tyrosine kinase inhibitor pool using analog-sensitive kinase technology

Zhenfan Wang, Minjun Jiang, Ninghan Feng and Chen Li

Biochimie, 2018, 152, 188
DOI: 10.1016/j.biochi.2018.07.005

Rational cyclization-based minimization of entropy penalty upon the binding of Nrf2-derived linear peptides to Keap1: A new strategy to improve therapeutic peptide activity against sepsis

Ke Chen, Liuliu Huang and Bin Shen

Biophysical Chemistry, 2019, 244, 22
DOI: 10.1016/j.bpc.2018.11.002

Rational redesign of a cation···π···π stacking at cardiovascular Fbw7–Skp1 complex interface and its application for deriving self-inhibitory peptides to disrupt the complex interaction

Jing Zhou and Yao-Sheng Wang

J Mol Model, 2017, 23
DOI: 10.1007/s00894-017-3456-z

Exploiting the chemical diversity space of phosphopeptide binding to nasopharyngeal carcinoma PLK1 PBD domain with unnatural amino acid building blocks by using QSAR-based genetic optimization

R.Y. Ma, J. Yang, J.J. Wu and H.Y. Zhu

SAR and QSAR in Environmental Research, 2024, 35, 899
DOI: 10.1080/1062936X.2024.2418355

Systematic molecular profiling of inhibitor response to the clinical missense mutations of ErbB family kinases in human gastric cancer

Xi Ding, Cheng Tong, Rong Chen, Xi Wang, Dongyun Gao and Lixia Zhu

Journal of Molecular Graphics and Modelling, 2020, 96, 107526
DOI: 10.1016/j.jmgm.2019.107526

Design, cyclization, and optimization of MMP13–TIMP1 interaction-derived self-inhibitory peptides against chondrocyte senescence in osteoarthritis

Wei Zhang, Chi Zhang, Congfeng Luo, Yulin Zhan and Biao Zhong

International Journal of Biological Macromolecules, 2019, 121, 921
DOI: 10.1016/j.ijbiomac.2018.10.141

Structure-Based Stepwise Screening of PPARγ Antagonists as Potential Competitors with NCOA1 Coactivator Peptide for PPARγ CIS Site

Yi Shen, Hongbo Chi, Jinhu Zhou, Lifei Luo, Qian Tu, Cancan Qi and Zuhua Gao

Int J Pept Res Ther, 2019, 25, 1369
DOI: 10.1007/s10989-018-9782-x

Drug–Target Association Kinetics in Drug Discovery

Adriaan P. IJzerman and Dong Guo

Trends in Biochemical Sciences, 2019, 44, 861
DOI: 10.1016/j.tibs.2019.04.004

Targeting Human Hippo TEAD Binding Interface with YAP/TAZ-Derived, Flexibility-Reduced Peptides in Gastric Cancer

Dejun Wu, Lijuan Luo, Zhou Yang, Yusheng Chen, Yingjun Quan and Zhijun Min

Int J Pept Res Ther, 2021, 27, 119
DOI: 10.1007/s10989-020-10069-9

Rational identification of natural organic compounds to target the intermolecular interaction between Foxm and DNA in colorectal cancer

Chunling Dong, Peng Yan, Juxun Wang, Hailian Mu, Shuli Wang and Fangchun Guo

Bioorganic Chemistry, 2017, 70, 12
DOI: 10.1016/j.bioorg.2016.11.003

Integrated unsupervised–supervised modeling and prediction of protein–peptide affinities at structural level

Peng Zhou, Li Wen, Jing Lin, Li Mei, Qian Liu, Shuyong Shang, Juelin Li and Jianping Shu

Briefings in Bioinformatics, 2022, 23
DOI: 10.1093/bib/bbac097

Machine learning‐based genetic evolution of antitumor proteins containing unnatural amino acids by integrating chemometric modeling and cytotoxicity analysis

Yongkang He and Luoluo Gao

Journal of Chemometrics, 2018, 32
DOI: 10.1002/cem.2974

Rational design of type-IA receptor-derived cyclic peptides to target human bone morphogenic protein 2

Xiaohua Fan, Hai Xia, Xiaoyun Liu, Benying Li and Jun Fang

J Biosci, 2019, 44
DOI: 10.1007/s12038-019-9945-8

Rational Design of the Minimal Requirement for Helix–Helix Peptide Interactions in the Trimer-of-Hairpins Motif of Pediatric Pneumonia RSV Fusion Glycoprotein

Daocheng Bao, Hongliang Bian, Darong Xu, Chunyang Zhao, Qing Jin, Min Zhu, Tingting Tao and Jinlan Cai

Int J Pept Res Ther, 2019, 25, 1087
DOI: 10.1007/s10989-018-9756-z