ZDOCK: An initial‐stage protein‐docking algorithm

Chen, Rong, Li, Li, Weng, Zhiping·2003·Proteins: Structure, Function, and Bioinformatics

Cited by (1,002)

Items 801–900 of 1,002

  1. Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex
    Warachai Praditwongwan, Phimonphan Chuankhayan, Somphot Saoin, Tanchanok Wisitponchai, Vannajan Sanghiran Lee, Sawitree Nangola, Saw See Hong, Philippe Minard, Pierre A. Boulanger, Chun‐Jung Chen et al. · 2014 · Journal of Computer-Aided Molecular Design
  2. Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes
    Nobuyuki Uchikoga, Takatsugu Hirokawa · 2010 · BMC Bioinformatics
  3. Exploring Angular Distance in Protein-Protein Docking Algorithms
    Thom Vreven, Howook Hwang, Zhiping Weng · 2013 · PLoS ONE
  4. Re-Docking Scheme for Generating Near-Native Protein Complexes by Assembling Residue Interaction Fingerprints
    Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama · 2013 · PLoS ONE
  5. Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures
    Surabhi Maheshwari, Michał Bryliński · 2015 · BMC Structural Biology
  6. Discovery of Functional Motifs from the Interface Region of Oligomeric Proteins Using Frequent Subgraph Mining
    Tanay Kumar Saha, Ataur Katebi, Wajdi Dhifli, Mohammad Al Hasan · 2017 · IEEE Transactions on Computational Biology and Bioinformatics
  7. Optimization of a MT1-MMP-targeting Peptide and Its Application in Near-infrared Fluorescence Tumor Imaging
    Li Ren, Ye Wang, Lei Zhu, Liqiao Shen, Jinrui Zhang, Jingjing Wang, Haolong Li, Qing‐Chuan Zheng, Dahai Yu, Xuexun Fang · 2018 · Scientific Reports
  8. Template‐based modeling and ab‐initio docking using CoDock in CAPRI
    Ren Kong, Ran‐Ran Liu, Ximing Xu, Dawei Zhang, Xiaoshuang Xu, Hang Shi, Shan Chang · 2020 · Proteins Structure Function and Bioinformatics
  9. Split-enzyme immunoassay to monitor EGFR-HER2 heterodimerization on cell surfaces
    Sun Jin Kim, Andrew S. Dixon, Shawn C. Owen · 2021 · Acta Biomaterialia
  10. Harnessing the functional diversity of plant cystatins to design inhibitor variants highly active against herbivorous arthropod digestive proteases
    Jonathan Tremblay, Marie‐Claire Goulet, Juan Vorster, Charles Goulet, Dominique Michaud · 2021 · FEBS Journal
  11. Targeting rho guanine nucleotide exchange factor ARHGEF5/TIM with auto-inhibitory peptides in human breast cancer
    Ou Huang, Dandan Wu, Feiyan Xie, Lili Lin, Xiaobo Wang, Min Jiang, Yafen Li, Weiguo Chen, Kunwei Shen, Xiaoqu Hu · 2015 · Amino Acids
  12. PHARMACOPHORE ELUCIDATION AND DOCKING STUDIES ON ANTI-INFLAMMATORY COMPOUNDS OF MEDICINAL PLANTS FOR ULCERATIVE COLITIS
    N S Hamsa, Vandana P Nair, Vivek Chandramohan, Seema J Patel · 2013 · Asian Journal of Pharmaceutical and Clinical Research
  13. Characterization of Kbot21 Reveals Novel Side Chain Interactions of Scorpion Toxins Inhibiting Voltage-Gated Potassium Channels
    Rym ElFessi-Magouri, Steve Peigneur, Houcemeddine Othman, Najet Srairi‐Abid, Mohamed El Ayeb, Jan Tytgat, Riadh Kharrat · 2015 · PLoS ONE
  14. Role of Interaction and Nucleoside Diphosphate Kinase B in Regulation of the Cystic Fibrosis Transmembrane Conductance Regulator Function by cAMP-Dependent Protein Kinase A
    Lee Anthony Borthwick, Mathieu Kerbiriou, Christopher J. Taylor, Giorgio Cozza, Ioan Lascu, Edith H. Postel, Diane M. Cassidy, Pascal Trouvé, Anil Mehta, Louise Robson et al. · 2016 · PLoS ONE
  15. Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle
    Angshuman Bagchi · 2012 · Molecular Biology Reports
  16. A novel homozygous mutation disrupting the initiation codon in the SLURP1 gene underlies mal de Meleda in a consanguineous family
    Khadim Shah, Abdul Nasır, Irfanullah Irfanullah, Shaheen Shahzad, Saadullah Khan, Wasim Ahmad · 2016 · Clinical and Experimental Dermatology
  17. HBD-2 variants and SARS-CoV-2: New insights into inter-individual susceptibility
    Mohammed Y. Behairy, Mohamed A. Soltan, Muhammad Alaa Eldeen, Jawaher Abdualbaqi Abdulhakim, Maryam M. Alnoman, Mohamed M. Abdel‐Daim, Hassan M. Otifi, Saleh M. Al‐Qahtani, Mohamed Samir Ahmed Zaki, Ghadi Alsharif et al. · 2022 · Frontiers in Immunology
  18. SPOP-mediated RIPK3 destabilization desensitizes LPS/sMAC/zVAD-induced necroptotic cell death
    Ga-Eun Lee, Geul Bang, Jiin Byun, Weidong Chen, Dohyun Jeung, Hana Cho, Joo Young Lee, Han Chang Kang, Hye Suk Lee, Jin Young Kim et al. · 2024 · Cellular and Molecular Life Sciences
  19. The multimerization pathway of the glucocorticoid receptor
    Andrea Alegre‐Martí, Alba Jiménez‐Panizo, Agustina L. Lafuente, Thomas A. Johnson, Inés Montoya-Novoa, Maria Nuria Peralta-Moreno, Pilar Montanyà-Valluguera, Josep Ponsetí-Pons, Montserrat Abella, Sohyoung Kim et al. · 2025 · Nucleic Acids Research
  20. Prediction of Protein-Protein Binding Interfaces
    Damian Marchewka, Wiktor Jurkowski, Mateusz Banach, Irena Roterman‐Konieczna · 2012 · Focus on structural biology
  21. Biological function derived from predicted structures in CASP11
    Peter J. Huwe, Qifang Xu, Maxim V. Shapovalov, Vivek Modi, Mark Andrake, Roland L. Dunbrack · 2016 · Proteins Structure Function and Bioinformatics
  22. Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations
    Didier Barradas‐Bautista, Juan Fernández‐Recio · 2017 · PLoS ONE
  23. On identifying collective displacements in apo-proteins that reveal eventual binding pathways
    Dube Dheeraj Prakashchand, Navjeet Ahalawat, Himanshu Khandelia, Jagannath Mondal, Surajit Sengupta · 2019 · PLoS Computational Biology
  24. Insights into the binding mode and functional components of the analgesic-antitumour peptide from Buthus martensii Karsch to human voltage-gated sodium channel 1.7 based on dynamic simulation analysis
    Fan Zhao, Jinlong Wang, Hong-Yan Ming, Yanan Zhang, Ying-Qiao Dun, Jinghai Zhang, Yongbo Song · 2019 · Journal of Biomolecular Structure and Dynamics
  25. evERdock BAI: Machine-learning-guided selection of protein-protein complex structure
    Kei Terayama, Ai Shinobu, Koji Tsuda, Kazuhiro Takemura, Akio Kitao · 2019 · The Journal of Chemical Physics
  26. Protein–protein docking with interface residue restraints*
    Hao Li, Sheng‐You Huang · 2020 · Chinese Physics B
  27. Discovery of traditional Chinese medicines against porcine reproductive and respiratory syndrome virus
    Wenqiang Cui, Fei Yu, Yuefeng Zhang, Xiao Han, Rongfeng Zou, Yan‐Dong Tang, Linguang Wang, Nsabimana Eliphaz, Jian Wang, Shuguang Yuan et al. · 2021 · Pharmacological Research - Modern Chinese Medicine
  28. Functional rewiring of G protein-coupled receptor signaling in human labor
    Abigail R. Walker, Camilla Bøgelund Larsen, Samit Kundu, Christina Stavrinidis, Sung Hye Kim, Asuka Inoue, David F. Woodward, Yun Sok Lee, Roberta Migale, David A. MacIntyre et al. · 2022 · Cell Reports
  29. Profiling Substrate Specificity of the SUMO Protease Ulp1 by the YESS–PSSC System to Advance the Conserved Mechanism for Substrate Cleavage
    Faying Zhang, Hui Zheng, Yufan Xian, Haoyue Song, Shengchen Wang, Yueli Yun, Yi Li, Guimin Zhang · 2022 · International Journal of Molecular Sciences
  30. Molecular Cloning, Expression, Sequence Characterization and Structural Insight of Bubalus bubalis Growth Hormone-Receptor
    Roquyya Gul, Muhammad Umair Hanif, Faiza Gul, Hafiz Muzzammel Rehman, Mahjabeen Saleem, Muhammad Sarfaraz Ahmad, Muhammad Usman Mirza · 2022 · Molecular Biotechnology
  31. Exploring the Pivotal Components Influencing the Side Effects Induced by an Analgesic-Antitumor Peptide from Scorpion Venom on Human Voltage-Gated Sodium Channels 1.4 and 1.5 through Computational Simulation
    Fan Zhao, Liangyi Fang, Qi Wang, Qi Ye, Yanan He, Weizhuo Xu, Yongbo Song · 2022 · Toxins
  32. Comprehensive study of rice YABBY gene family: evolution, expression and interacting proteins analysis
    Ting Zhang, Anqi Wu, Xiaosong Hu, Qiyu Deng, Ziyi Ma, Lina Su · 2023 · PeerJ
  33. An Immuno-informatics driven Epitope study from the molecular interaction of JEV non-structural (NS) proteins with Ribophorin (RPN)
    Usman Sayeed, Gulshan Wadhwa, Mohammad Kalim Ahmad Khan, Qazi Mohammad Sajid Jamal, Salman Akhtar, M. Salman Khan · 2014 · Bioinformation
  34. pH-induced quaternary assembly of Vitreoscilla hemoglobin: The monomer exhibits better peroxidase activity
    Wei Li, Yubin Zhang, Haoran Xu, Lei Wu, Yufeng Cao, Haifeng Zhao, Zhengqiang Li · 2013 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
  35. Molecular Dynamic and Docking Interaction Study of Heterodera glycines Serine Proteinase with Vigna mungo Proteinase Inhibitor
    Chekkara Venkata Prasad, Saurabh K. Gupta, А. К. Гапоненко, Murlidhar Tiwari · 2013 · Applied Biochemistry and Biotechnology
  36. Optimization of protein–protein docking for predicting Fc–protein interactions
    Mark Agostino, Ricardo L. Mancera, Paul A. Ramsland, Juan Fernández‐Recio · 2016 · Journal of Molecular Recognition
  37. RK, the first scorpion peptide with dual disintegrin activity on α1β1 and αvβ3 integrins
    Oussema Khamessi, Hazem Ben Mabrouk, Houcemeddine Othman, Rym ElFessi-Magouri, Michel MDW DE WAARD, Hafedh Mejdoub, Naziha Marrakchi, Najet Srairi‐Abid, Riadh Kharrat · 2018 · International Journal of Biological Macromolecules
  38. Computational Modeling of Designed Ankyrin Repeat Protein Complexes with Their Targets
    Filip Radom, Emanuele Paci, Andreas Plückthun · 2019 · Journal of Molecular Biology
  39. EROS-DOCK: protein–protein docking using exhaustive branch-and-bound rotational search
    Maria Elisa Ruiz Echartea, Isaure Chauvot de Beauchêne, David W. Ritchie · 2019 · Bioinformatics
  40. Analysis of the TP53 Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach
    Kumaraswamy Naidu Chitrala, Mitzi Nagarkatti, Prakash S. Nagarkatti, Suneetha Yeguvapalli · 2019 · International Journal of Molecular Sciences
  41. Inhibition of Plasmodium falciparum cysteine protease falcipain-2 by a human cross-class inhibitor serpinB3: A mechanistic insight
    Benazir Alam, Sampa Biswas · 2019 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
  42. Molecular Recognition of Rhodopsin Kinase GRK1 and Recoverin Is Tuned by Switching Intra- and Intermolecular Electrostatic Interactions
    Seher Abbas, Valerio Marino, Daniele Dell’Orco, Karl‐Wilhelm Koch · 2019 · Biochemistry
  43. Phi class glutathione transferases as molecular targets towards multiple-herbicide resistance: Inhibition analysis and pharmacophore design
    Nikolaos Georgakis, Nirmal Poudel, Dimitriοs Vlachakis, Anastassios C. Papageorgiou, Nikolaos E. Labrou · 2020 · Plant Physiology and Biochemistry
  44. Immunoinformatic Approach to Contrive a Next Generation Multi-Epitope Vaccine Against Achromobacter xylosoxidans Infections
    K. Khalid, U. Saeed, M. Aljuaid, Mohammad Ali, Awais Anjum, Yasir Waheed · 2022 · Frontiers in Medicine
  45. Interaction of p53 with BRC analogs: A comparative design assisted by ZDOCK and CABS-Dock simulation
    Libo Yuan, Guangbin Liu, Dongxin Zhao, Hanjing Zhu, Jianzhao Qi, Kui Lü · 2022 · Journal of Molecular Structure
  46. Binding orientation and specificity of calmodulin to rat olfactory cyclic nucleotide-gated ion channel
    Deli Irene, Jian-Wen Huang, Tse-Yu Chung, Feng-Yin Li, Jason T. C. Tzen, Ta-Hsien Lin, Chia‐Lin Chyan · 2012 · Journal of Biomolecular Structure and Dynamics
  47. Versatile substrate protein recognition mechanism of the eukaryotic chaperonin CCT
    Manori Jayasinghe, Cody Tewmey, George Stan · 2009 · Proteins Structure Function and Bioinformatics
  48. Anticonvulsant Met-Enkephalin Analogues Containing Backbone Spacers Reveal Alternative Non-Opioid Signaling in the Brain
    Hee-Kyoung Lee, Misty D. Smith, Brian James Smith, Joel Grussendorf, Liping Xu, Robert J. Gillies, H. Steve White, Grzegorz W. Bulaj · 2009 · ACS Chemical Biology
  49. Molecular Docking of Known Carcinogen 4-(Methyl-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) with Cyclin Dependent Kinases towards Its Potential Role in Cell Cycle Perturbation
    Mohd Haneef, Mohtashim Lohani, Anupam Dhasmana, Qazi Mohammad Sajid Jamal, Sara Shahid, Sumbul Firdaus · 2014 · Bioinformation
  50. How to Use Not-Always-Reliable Binding Site Information in Protein-Protein Docking Prediction
    Lin Li, Yanzhao Huang, Yi Xiao · 2013 · PLoS ONE
  51. Molecular modeling, dynamics and docking studies of Purine Nucleoside Phosphorylase from Streptococcus pyogenes
    Luís Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres, Raquel Dias, Luiz Augusto Basso, Diógenes Santiago Santos, Walter Filgueira de Azevedo · 2009 · Biophysical Chemistry
  52. Selection of near‐native poses in CAPRI rounds 13‐19
    Sanbo Qin, Huan‐Xiang Zhou · 2010 · Proteins Structure Function and Bioinformatics
  53. Identification through Combinatorial Random and Rational Mutagenesis of a Substrate-interacting Exosite in the γ Domain of Streptokinase
    Suman Yadav, Rachna Aneja, Prakash Kumar, Manish Datt, Sonali Sinha, Girish Sahni · 2010 · Journal of Biological Chemistry
  54. Exploring protein–protein intermolecular recognition between meprin-α and endogenous protease regulator cystatinC coupled with pharmacophore elucidation
    Ankur Chaudhuri, Sampa Biswas, Sibani Sen Chakraborty · 2018 · Journal of Biomolecular Structure and Dynamics
  55. Structural Communication between the E. coli Chaperones DnaK and Hsp90
    Matthew P. Grindle, Ben Carter, John Paul Alao, Katherine Connors, Riina Tehver, Andrea N. Kravats · 2021 · International Journal of Molecular Sciences
  56. Interaction of malaria parasite‐inhibitory antibodies with the merozoite surface protein MSP119 by computational docking
    Flavia Autore, Sara Melchiorre, Jens Kleinjung, William D. Morgan, Franca Fraternali · 2006 · Proteins Structure Function and Bioinformatics
  57. DeepInterface: Protein-protein interface validation using 3D Convolutional Neural Networks
    A.T. Balci, Can Gümeli, Asma Hakouz, Deniz Yüret, Özlem Keskin, Attila Gürsoy · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  58. Automated and Efficient Generation of General Molecular Aggregate Structures
    Christoph Plett, Stefan Grimme · 2022 · Angewandte Chemie
  59. ClassyPose: A Machine‐Learning Classification Model for Ligand Pose Selection Applied to Virtual Screening in Drug Discovery
    Viet‐Khoa Tran‐Nguyen, Anne‐Claude Camproux, Olivier Taboureau · 2024 · Advanced Intelligent Systems
  60. Machine-learning-assisted high-throughput identification of potent and stable neutralizing antibodies against all four dengue virus serotypes
    Piyatida Natsrita, Phasit Charoenkwan, Watshara Shoombuatong, Panupong Mahalapbutr, Kiatichai Faksri, Sorujsiri Chareonsudjai, Thanyada Rungrotmongkol, Chonlatip Pipattanaboon · 2024 · Scientific Reports
  61. Exploring Bioinformatics Solutions for Improved Leishmaniasis Diagnostic Tools: A Review
    Natáli Tereza Capistrano Costa, Allana Maria de Souza Pereira, C. Mendes da Silva, Emanuelle Souza, Luiz Felipe Ferreira, Beatriz de Oliveira, Marcelo Zaldini Hernandes, Valéria Rêgo Alves Pereira · 2024 · Molecules
  62. Semaglutide Mitigates Ischemic Brain Injury by Inhibiting Ferroptosis via Modulation of FoXO1 and DRP1 Pathways
    Weihua Wang, Meng Pang, Yifeng Zhang, Shuai Hou, Yulei Xia, Youkui Shi, Xiaojun Zhang, Yanqiang Wang · 2025 · Molecular Neurobiology
  63. A basin hopping algorithm for protein-protein docking
    Irina Hashmi, Amarda Shehu · 2012 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  64. New insights of falcipain 2 structure from Plasmodium falciparum 3D7 strain
    Subhoja Chakraborty, Benazir Alam, Sampa Biswas · 2021 · Biochemical and Biophysical Research Communications
  65. Inclusion of Desolvation Energy into Protein–Protein Docking through Atomic Contact Potentials
    Hao Li, Yumeng Yan, Xuejun Zhao, Sheng‐You Huang · 2022 · Journal of Chemical Information and Modeling
  66. Classifying Protein–Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches
    Emma Goulard Coderc de Lacam, Benoı̂t Roux, Christophe J. Chipot · 2024 · Journal of Chemical Information and Modeling
  67. Analysis of the complex formation, interaction and electron transfer pathway between the “open” conformation of NADPH-cytochrome P450 reductase and aromatase
    Yuejie Dai, Jing Zhen, Xiuli Zhang, Yonghui Zhong, Shaodan Liu, Ziyue Sun, Yue Guo, Qingli Wu · 2015 · Steroids
  68. Deciphering the protein interaction in adhesion of Francisella tularensis subsp. holarctica to the endothelial cells
    Elena Bencúrová, Andrej Kováč, Lucia Pulzová, Miklós Gyuranecz, Patrik Mlynárčik, Rastislav Mucha, Dimitriοs Vlachakis, Σοφία Κοσσίδα, Zuzana Flachbartova, Mangesh Ramesh Bhide · 2015 · Microbial Pathogenesis
  69. Focused grid‐based resampling for protein docking and mapping
    Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sándor Vajda, Dima Kozakov · 2016 · Journal of Computational Chemistry
  70. Adenylate kinase potentiates the capsular polysaccharide by modulating Cps2D in Streptococcus pneumoniae D39
    Prachetash Ghosh, Truc Thanh Luong, Masaud Shah, Trung Thanh Thach, Sangdun Choi, Sangho Lee, Dong‐Kwon Rhee · 2018 · Experimental & Molecular Medicine
  71. 17-Hydroxy Wortmannin Restores TRAIL's Response by Ameliorating Increased Beclin 1 Level and Autophagy Function in TRAIL-Resistant Colon Cancer Cells
    Sheng Dai, Shu Yang, Xin Hu, Wei Sun, Gregory J. Tawa, Wenge Zhu, Aaron David Schimmer, Chao He, Bingliang Fang, Hongbo Zhu et al. · 2019 · Molecular Cancer Therapeutics
  72. Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening
    Xiaoqian Xu, Li Zhang, Ying Cai, Dongxin Liu, Zhengwen Shang, Qiuhong Ren, Qiong Li, Wei‐Dong Zhao, Yuhua Chen · 2019 · Journal of Computer-Aided Molecular Design
  73. Review About Bioinformatics, Databases, Sequence Alignment, Docking, and Drug Discovery
    P. Lakshmi, D. Ramyachitra · 2020 · Algorithms for intelligent systems
  74. Systematic protein-protein docking and molecular dynamics studies of HIV-1 gp120 and CD4: insights for new drug development.
    Teow Chong Teoh, Thorsten Heidelberg, Mohammed Rizman‐Idid · 2011 · Europe PMC (PubMed Central)
  75. Molecular simulation of model sulfated polysaccharides of low molecular weight from Ganoderma lucidum and their interaction with human serum albumin
    Jie Shen, Haijun Wang, Yongmei Xia · 2014 · Structural Chemistry
  76. Study of Recombinant Antibody Fragments and PAI-1 Complexes Combining Protein-Protein Docking and Results from Site-Directed Mutagenesis
    Héctor Novoa de Armas, Maarten Dewilde, Koen Verbeke, Marc De Maeyer, Paul J. Declerck · 2007 · Structure
  77. Computational prediction of protein-protein complexes
    Seema Mishra · 2012 · BMC Research Notes
  78. Molecular Simulation Methods for Selecting Thrombin-Binding Aptamers
    Jangam Vikram Kumar, Wen‐Yih Chen, Jeffrey J. P. Tsai, Wen-Pin Hu · 2013 · Lecture notes in electrical engineering
  79. Physico-chemical and in-silico analysis of a phytocystatin purified from Brassica juncea cultivar RoAgro 5444
    Shumaila Khan, Sabahuddin Ahmad, Mohammad Imran Siddiqi, Bilqees Bano · 2016 · Biochemistry and Cell Biology
  80. Template‐based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30
    Hasup Lee, Minkyung Baek, Gyu Rie Lee, Sangwoo Park, Chaok Seok · 2016 · Proteins Structure Function and Bioinformatics
  81. Coupling Drosophila melanogaster Cryptochrome Light Activation and Oxidation of the Kvβ Subunit Hyperkinetic NADPH Cofactor
    Gongyi Hong, Ruth Pachter, Thorsten Ritz · 2018 · The Journal of Physical Chemistry B
  82. Heat shock protein 90 enhances the electron transfer between the FMN and heme cofactors in neuronal nitric oxide synthase
    Huayu Zheng, Jinghui Li, Changjian Feng · 2020 · FEBS Letters
  83. Probing the Key Interactions between Human Atg5 and Atg16 Proteins: A Prospective Application of Molecular Modeling
    Zhixiong Zhao, Zhengxi Zhang, Yan Li, Mi Zhou, Xun Li, Biao Yu, Renxiao Wang · 2013 · ChemMedChem
  84. Sequence Alignment Reveals Possible MAPK Docking Motifs on HIV Proteins
    Perry Evans, Ahmet Saçan, Lyle Ungar, Aydın Tözeren · 2010 · PLoS ONE
  85. DEVELOPMENT OF AN AFFINITY EVALUATION AND PREDICTION SYSTEM BY USING THE SHAPE COMPLEMENTARITY CHARACTERISTIC BETWEEN PROTEINS
    Koki Tsukamoto, Tatsuya Yoshikawa, Yuichiro Hourai, Kazuhiko Fukui, Yutaka Akiyama · 2008 · Journal of Bioinformatics and Computational Biology
  86. Structural characterization of the functional regions in the archaeal protein Sso7d
    Giovanni Renzone, Rosa Maria Vitale, Andrea Scaloni, Mosé Rossi, Pietro Amodeo, Annamaria Guagliardi · 2007 · Proteins Structure Function and Bioinformatics
  87. Novel single-domain antibodies targeting a unique transferrin receptor 1 epitope for cross-species delivery of drugs in the central nervous system
    Marion David, Romy Cohen, Diane Beuzelin, Géraldine Ferracci, Marina Cresci, Aude Faucon, Karima Abouzid, Gersande Godefroy, Maxime Masse, Yasmine Mechioukhi et al. · 2025 · Journal of Controlled Release
  88. GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing
    Alexander A. Kantardjiev · 2011 · Nucleic Acids Research
  89. SurfPro-NN: A 3D point cloud neural network for the scoring of protein–protein docking models based on surfaces features and protein language models
    Qianli Yang, Xiaocheng Jin, Haixia Zhou, Junjie Ying, Jiajun Zou, Yiyang Liao, Xiaoli Lu, Shengxiang Ge, Hai Jing Yu, Xiaoping Min · 2024 · Computational Biology and Chemistry
  90. Protein docking with information on evolutionary conserved interfaces
    Irina Hashmi, Bahar Akbal-Delibas, Nurit Haspel, Amarda Shehu · 2011 · IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
  91. Analysis of a single-codon E746 deletion in exon 19 of the epidermal growth factor receptor
    Masahito Ogasawara, Yutaka Nakamura, Naoto Morikawa, Hiroo Nitanai, Satoshi Moriguchi, Ryosuke Chiba, Heisuke Saito, Mika Ohta, Tatsuo Tanita, Tamotsu Sugai et al. · 2016 · Cancer Chemotherapy and Pharmacology
  92. Bioinformatics exploration of PAK1 (P21-activated kinase-1) revealed potential network gene elements in breast invasive carcinoma
    Nanda Kumar Yellapu, Madhusudana Pulaganti, Suresh B. Pakala · 2016 · Journal of Biomolecular Structure and Dynamics
  93. The antitumor activity and preliminary modeling on the potential mechanism of action of human peroxiredoxin-5
    Juanjuan Liu, Xiaozhou Feng, Yuanyuan Jin, Zhengyang Sun, Haoyi Meng, Zhi-Fei Zhang, Laixing Hu, Zhaoyong Yang · 2017 · Oncotarget
  94. The Negative Effects of KPN00353 on Glycerol Kinase and Microaerobic 1,3-Propanediol Production in Klebsiella pneumoniae
    W.Y. Jeng, Novaria Sari Dewi Panjaitan, Yu‐Tze Horng, Wen-Ting Chung, Chih‐Ching Chien, Po‐Chi Soo · 2017 · Frontiers in Microbiology
  95. Interaction of S17 Antibody with the Functional Binding Region of the Hepatitis B Virus Pre-S2 Epitope
    Chang-Yu Chang, Fu-Ling Chang, Chen-Wei Chiang, Yan-Ni Lo, Tsai-Yu Lin, Wang-Chuan Chen, Keng‐Chang Tsai, Yu‐Ching Lee · 2018 · Viral Immunology
  96. Improved cluster ranking in protein–protein docking using a regression approach
    Shahabeddin Sotudian, Israel Desta, Nasser Hashemi, Shahrooz Zarbafian, Dima Kozakov, Pirooz Vakili, Sándor Vajda, Ioannis Ch. Paschalidis · 2021 · Computational and Structural Biotechnology Journal
  97. Exploring effectiveness of ab-initio protein–protein docking methods on a novel antibacterial protein complex dataset
    Wei Zhang, Qiaozhen Meng, Jijun Tang, Fei Guo · 2021 · Briefings in Bioinformatics
  98. Virtual Evolution of HVEM Segment for Checkpoint Inhibitor Discovery
    Mingjia Yu, Huimin Zhao, Yuhui Miao, Shizhong Luo, Song Xue · 2021 · International Journal of Molecular Sciences
  99. GalaxyDomDock: An Ab Initio Domain–domain Docking Web Server for Multi-domain Protein Structure Prediction
    Jayun Choi, Taeyong Park, Seung-Yul Lee, Jinsol Yang, Chaok Seok · 2022 · Journal of Molecular Biology
  100. MxB Disrupts Hepatitis C Virus NS5A–CypA Complex: Insights From a Combined Theoretical and Experimental Approach
    Quanjie Li, Ni A. An, Xiao Yin, Ruixin Zhang, Huihan Shao, Dongrong Yi, Shan Cen · 2022 · Frontiers in Microbiology