ACS Publications. Most Trusted. Most Cited. Most Read
Combining Global and Local Measures for Structure-Based Druggability Predictions

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Chem. Inf. Model. 2012, 52, 2, 360-372
    Article

    Combining Global and Local Measures for Structure-Based Druggability Predictions
    Click to copy article linkArticle link copied!

    View Author Information
    † University of Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
    ‡ Merck KGaA, Merck Serono, Global Computational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany
    § Merck KGaA, Merck Serono, Bioinformatics, Frankfurter Str. 250, 64293 Darmstadt, Germany
    *E-mail: [email protected]
    Other Access Options

    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2012, 52, 2, 360–372
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ci200454v
    Published December 8, 2011
    Copyright © 2011 American Chemical Society
    Request reuse permissions

    Abstract

    Click to copy section linkSection link copied!
    Abstract Image

    Predicting druggability and prioritizing certain disease modifying targets for the drug development process is of high practical relevance in pharmaceutical research. DoGSiteScorer is a fully automatic algorithm for pocket and druggability prediction. Besides consideration of global properties of the pocket, also local similarities shared between pockets are reflected. Druggability scores are predicted by means of a support vector machine (SVM), trained, and tested on the druggability data set (DD) and its nonredundant version (NRDD). The DD consists of 1069 targets with assigned druggable, difficult, and undruggable classes. In 90% of the NRDD, the SVM model based on global descriptors correctly classifies a target as either druggable or undruggable. Nevertheless, global properties suffer from binding site changes due to ligand binding and from the pocket boundary definition. Therefore, local pocket properties are additionally investigated in terms of a nearest neighbor search. Local similarities are described by distance dependent histograms between atom pairs. In 88% of the DD pocket set, the nearest neighbor and the structure itself conform with their druggability type. A discriminant feature between druggable and undruggable pockets is having less short-range hydrophilic–hydrophilic pairs and more short-range lipophilic–lipophilic pairs. Our findings for global pocket descriptors coincide with previously published methods affirming that size, shape, and hydrophobicity are important global pocket descriptors for automatic druggability prediction. Nevertheless, the variety of pocket shapes and their flexibility upon ligand binding limit the automatic projection of druggable features onto descriptors. Incorporating local pocket properties is another step toward a reliable descriptor-based druggability prediction.

    Copyright © 2011 American Chemical Society

    Subjects

    what are subjects

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. Add or change your institution or let them know you’d like them to include access.

    Cited By

    Click to copy section linkSection link copied!

    This article is cited by 332 publications.

    1. Nan Lv, Zexing Cao. Subpocket-Based Analysis Approach for the Protein Pocket Dynamics. Journal of Chemical Theory and Computation 2024, 20 (11) , 4909-4920. https://doi.org/10.1021/acs.jctc.4c00476
    2. Samuel R. Costa, Andreanne G. Vasconcelos, José Otávio C. S. Almeida, Daniel D. R. Arcanjo, Anderson Dematei, Eder A. Barbosa, Pedro Costa Silva, Thiago Nascimento, Lucianna H. Santos, Peter Eaton, José Roberto S. de A. Leite, Guilherme D. Brand. Structural Characterization and Rat Aortic Vascular Reactivity of Bradykinin-Potentiating Peptides (BPPs) from the Snake Venom of Bothrops moojeni from Delta do Parnaíba Region, Brazil. Journal of Natural Products 2024, 87 (4) , 820-830. https://doi.org/10.1021/acs.jnatprod.3c00991
    3. Yeju Kim, Ceyhun Bereketoglu, Onur Sercinoglu, Ajay Pradhan. In Vitro, In Vivo, and In Silico Analysis of Pyraclostrobin and Cyprodinil and Their Mixture Reveal New Targets and Signaling Mechanisms. Chemical Research in Toxicology 2024, 37 (3) , 497-512. https://doi.org/10.1021/acs.chemrestox.3c00371
    4. Mengrong Li, Xiaoxiao Zhang, Shu Li, Jingjing Guo. Unraveling the Interplay of Extracellular Domain Conformational Changes and Parathyroid Hormone Type 1 Receptor Activation in Class B1 G Protein-Coupled Receptors: Integrating Enhanced Sampling Molecular Dynamics Simulations and Markov State Models. ACS Chemical Neuroscience 2024, 15 (4) , 844-853. https://doi.org/10.1021/acschemneuro.3c00747
    5. Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey. Redocking the PDB. Journal of Chemical Information and Modeling 2024, 64 (1) , 219-237. https://doi.org/10.1021/acs.jcim.3c01573
    6. Lucas G. Viviani, Daria B. Kokh, Rebecca C. Wade, Antonia T.-do Amaral. Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics. Journal of Chemical Information and Modeling 2023, 63 (15) , 4691-4707. https://doi.org/10.1021/acs.jcim.3c01068
    7. Luca Gagliardi, Walter Rocchia. SiteFerret: Beyond Simple Pocket Identification in Proteins. Journal of Chemical Theory and Computation 2023, 19 (15) , 5242-5259. https://doi.org/10.1021/acs.jctc.2c01306
    8. Javier Vázquez, Tiziana Ginex, Albert Herrero, Christophe Morisseau, Bruce D. Hammock, F. Javier Luque. Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits. Journal of Chemical Information and Modeling 2023, 63 (10) , 3209-3225. https://doi.org/10.1021/acs.jcim.3c00301
    9. Joel Graef, Christiane Ehrt, Matthias Rarey. Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. Journal of Chemical Information and Modeling 2023, 63 (10) , 3128-3137. https://doi.org/10.1021/acs.jcim.3c00336
    10. Ashima Chopra, Joseph D. Bauman, Francesc X. Ruiz, Eddy Arnold. Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening. Journal of Medicinal Chemistry 2023, 66 (9) , 6013-6024. https://doi.org/10.1021/acs.jmedchem.2c01681
    11. Christian Kersten, Steven Clower, Fabian Barthels. Hic Sunt Dracones: Molecular Docking in Uncharted Territories with Structures from AlphaFold2 and RoseTTAfold. Journal of Chemical Information and Modeling 2023, 63 (7) , 2218-2225. https://doi.org/10.1021/acs.jcim.2c01400
    12. Carlos Sicilia, Andrés Corral-Lugo, Pawel Smialowski, Michael J. McConnell, Antonio J. Martín-Galiano. Unsupervised Machine Learning Organization of the Functional Dark Proteome of Gram-Negative “Superbugs”: Six Protein Clusters Amenable for Distinct Scientific Applications. ACS Omega 2022, 7 (50) , 46131-46145. https://doi.org/10.1021/acsomega.2c04076
    13. Janis Müller, Raphael Klein, Olga Tarkhanova, Anastasiia Gryniukova, Petro Borysko, Stefan Merkl, Moritz Ruf, Alexander Neumann, Marcus Gastreich, Yurii S. Moroz, Gerhard Klebe, Serghei Glinca. Magnet for the Needle in Haystack: “Crystal Structure First” Fragment Hits Unlock Active Chemical Matter Using Targeted Exploration of Vast Chemical Spaces. Journal of Medicinal Chemistry 2022, 65 (23) , 15663-15678. https://doi.org/10.1021/acs.jmedchem.2c00813
    14. Mei Fang, Quan Zhang, Xin Wang, Kehe Su, Ping Guan, Xiaoling Hu. Inhibition Mechanisms of (−)-Epigallocatechin-3-gallate and Genistein on Amyloid-beta 42 Peptide of Alzheimer’s Disease via Molecular Simulations. ACS Omega 2022, 7 (23) , 19665-19675. https://doi.org/10.1021/acsomega.2c01412
    15. Joel Graef, Christiane Ehrt, Konrad Diedrich, Martin Poppinga, Norbert Ritter, Matthias Rarey. Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase Structures. Journal of Medicinal Chemistry 2022, 65 (2) , 1384-1395. https://doi.org/10.1021/acs.jmedchem.1c01046
    16. Jianyu Li, Aurélien F. A. Moumbock, Ammar Qaseem, Qianqing Xu, Yue Feng, Dan Wang, Stefan Günther. AroCageDB: A Web-Based Resource for Aromatic Cage Binding Sites and Their Intrinsic Ligands. Journal of Chemical Information and Modeling 2021, 61 (11) , 5327-5330. https://doi.org/10.1021/acs.jcim.1c00927
    17. Daniel J. Evans, Remy A. Yovanno, Sanim Rahman, David W. Cao, Morgan Q. Beckett, Milan H. Patel, Afif F. Bandak, Albert Y. Lau. Finding Druggable Sites in Proteins Using TACTICS. Journal of Chemical Information and Modeling 2021, 61 (6) , 2897-2910. https://doi.org/10.1021/acs.jcim.1c00204
    18. Muhammad Imran, Fawad Ali Shah, Humaira Nadeem, Alam Zeb, Muhammad Faheem, Shagufta Naz, Asma Bukhari, Tahir Ali, Shupeng Li. Synthesis and Biological Evaluation of Benzimidazole Derivatives as Potential Neuroprotective Agents in an Ethanol-Induced Rodent Model. ACS Chemical Neuroscience 2021, 12 (3) , 489-505. https://doi.org/10.1021/acschemneuro.0c00659
    19. Gerard Martinez-Rosell, Silvia Lovera, Zara A. Sands, Gianni De Fabritiis. PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations. Journal of Chemical Information and Modeling 2020, 60 (4) , 2314-2324. https://doi.org/10.1021/acs.jcim.9b01209
    20. Jui-Hung Yuan, Sungho Bosco Han, Stefan Richter, Rebecca C. Wade, Daria B. Kokh. Druggability Assessment in TRAPP Using Machine Learning Approaches. Journal of Chemical Information and Modeling 2020, 60 (3) , 1685-1699. https://doi.org/10.1021/acs.jcim.9b01185
    21. Benedikt Millies, Franziska von Hammerstein, Andrea Gellert, Stefan Hammerschmidt, Fabian Barthels, Ulrike Göppel, Melissa Immerheiser, Fabian Elgner, Nathalie Jung, Michael Basic, Christian Kersten, Werner Kiefer, Jochen Bodem, Eberhard Hildt, Maike Windbergs, Ute A. Hellmich, Tanja Schirmeister. Proline-Based Allosteric Inhibitors of Zika and Dengue Virus NS2B/NS3 Proteases. Journal of Medicinal Chemistry 2019, 62 (24) , 11359-11382. https://doi.org/10.1021/acs.jmedchem.9b01697
    22. Zhaoqiang Chen, Xinben Zhang, Cheng Peng, Jinan Wang, Zhijian Xu, Kaixian Chen, Jiye Shi, Weiliang Zhu. D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. Journal of Chemical Information and Modeling 2019, 59 (8) , 3353-3358. https://doi.org/10.1021/acs.jcim.9b00332
    23. Bin Chong, Maodong Li, Tong Li, Miao Yu, Yugang Zhang, Zhirong Liu. Conservation of Potentially Druggable Cavities in Intrinsically Disordered Proteins. ACS Omega 2018, 3 (11) , 15643-15652. https://doi.org/10.1021/acsomega.8b02092
    24. M. Yagiz Unver, Robin M. Gierse, Harry Ritchie, Anna K. H. Hirsch. Druggability Assessment of Targets Used in Kinetic Target-Guided Synthesis. Journal of Medicinal Chemistry 2018, 61 (21) , 9395-9409. https://doi.org/10.1021/acs.jmedchem.8b00266
    25. Xiaodong Ren, Yu-Sheng Shi, Yan Zhang, Bin Liu, Li-Hong Zhang, Yu-Bo Peng, Rui Zeng. Novel Consensus Docking Strategy to Improve Ligand Pose Prediction. Journal of Chemical Information and Modeling 2018, 58 (8) , 1662-1668. https://doi.org/10.1021/acs.jcim.8b00329
    26. Therese Inhester, Stefan Bietz, Matthias Hilbig, Robert Schmidt, and Matthias Rarey . Index-Based Searching of Interaction Patterns in Large Collections of Protein–Ligand Interfaces. Journal of Chemical Information and Modeling 2017, 57 (2) , 148-158. https://doi.org/10.1021/acs.jcim.6b00561
    27. Bradley C. Doak, Jie Zheng, Doreen Dobritzsch, and Jan Kihlberg . How Beyond Rule of 5 Drugs and Clinical Candidates Bind to Their Targets. Journal of Medicinal Chemistry 2016, 59 (6) , 2312-2327. https://doi.org/10.1021/acs.jmedchem.5b01286
    28. Andrea Volkamer, Sameh Eid, Samo Turk, Friedrich Rippmann, and Simone Fulle . Identification and Visualization of Kinase-Specific Subpockets. Journal of Chemical Information and Modeling 2016, 56 (2) , 335-346. https://doi.org/10.1021/acs.jcim.5b00627
    29. Dima Kozakov, David R. Hall, Raeanne L. Napoleon, Christine Yueh, Adrian Whitty, and Sandor Vajda . New Frontiers in Druggability. Journal of Medicinal Chemistry 2015, 58 (23) , 9063-9088. https://doi.org/10.1021/acs.jmedchem.5b00586
    30. David Rooklin, Cheng Wang, Joseph Katigbak, Paramjit S. Arora, and Yingkai Zhang . AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces. Journal of Chemical Information and Modeling 2015, 55 (8) , 1585-1599. https://doi.org/10.1021/acs.jcim.5b00103
    31. Alexandre Borrel, Leslie Regad, Henri Xhaard, Michel Petitjean, and Anne-Claude Camproux . PockDrug: A Model for Predicting Pocket Druggability That Overcomes Pocket Estimation Uncertainties. Journal of Chemical Information and Modeling 2015, 55 (4) , 882-895. https://doi.org/10.1021/ci5006004
    32. Andrea Volkamer, Sameh Eid, Samo Turk, Sabrina Jaeger, Friedrich Rippmann, and Simone Fulle . Pocketome of Human Kinases: Prioritizing the ATP Binding Sites of (Yet) Untapped Protein Kinases for Drug Discovery. Journal of Chemical Information and Modeling 2015, 55 (3) , 538-549. https://doi.org/10.1021/ci500624s
    33. Rémi Cuchillo, Kevin Pinto-Gil, and Julien Michel . A Collective Variable for the Rapid Exploration of Protein Druggability. Journal of Chemical Theory and Computation 2015, 11 (3) , 1292-1307. https://doi.org/10.1021/ct501072t
    34. Timo Krotzky, Thomas Rickmeyer, Thomas Fober, and Gerhard Klebe . Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple Due to Inherent Shape Similarity. Journal of Chemical Information and Modeling 2014, 54 (11) , 3229-3237. https://doi.org/10.1021/ci500553a
    35. Lewis R. Vidler, Nathan Brown, Stefan Knapp, and Swen Hoelder . Druggability Analysis and Structural Classification of Bromodomain Acetyl-lysine Binding Sites. Journal of Medicinal Chemistry 2012, 55 (17) , 7346-7359. https://doi.org/10.1021/jm300346w
    36. Guangtao Zhang, Roberto Sanchez, and Ming-Ming Zhou . Scaling the Druggability Landscape of Human Bromodomains, a New Class of Drug Targets. Journal of Medicinal Chemistry 2012, 55 (17) , 7342-7345. https://doi.org/10.1021/jm3011977
    37. Jérémy Desaphy, Karima Azdimousa, Esther Kellenberger, and Didier Rognan . Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes. Journal of Chemical Information and Modeling 2012, 52 (8) , 2287-2299. https://doi.org/10.1021/ci300184x
    38. Emanuele Perola, Lee Herman, and Jonathan Weiss . Development of a Rule-Based Method for the Assessment of Protein Druggability. Journal of Chemical Information and Modeling 2012, 52 (4) , 1027-1038. https://doi.org/10.1021/ci200613b
    39. Bin Fang, Hua Bai, Jiaxin Zhang, Limin Wang, PanPan Li, Yihao Ge, Hui Yang, Hui Wang, Bo Peng, Wenbo Hu, Huili Ma, Xi Chen, Li Fu, Lin Li. Albumins constrainting the conformation of mitochondria-targeted photosensitizers for tumor-specific photodynamic therapy. Biomaterials 2025, 315 , 122914. https://doi.org/10.1016/j.biomaterials.2024.122914
    40. Yuhang Liu, Shuangyan Zhou, Zhe Qiang, Shuyi Wu, Chunyan Zhang, Quan Sun, Xiaohong He, Pingan Chang, Huimin Pang. The enhancement mechanisms of chondroitin sulfate on α-amylase activity: Exploring the interaction using in vitro and in silico studies. Food Chemistry 2025, 466 , 142230. https://doi.org/10.1016/j.foodchem.2024.142230
    41. Aamir R. Shama, Mehulkumar L. Savaliya. Benzothiazole-triazole hybrids: Novel anticancer agents inducing cell cycle arrest and apoptosis through Bcl-2 inhibition in triple-negative breast cancer. Bioorganic Chemistry 2025, 155 , 108150. https://doi.org/10.1016/j.bioorg.2025.108150
    42. Sajjad Haider, Mamona Mushtaq, Mohammad Nur-e-Alam, Aftab Ahmed, Zaheer Ul-Haq. Identification of novel small molecule inhibitors for solute carrier SGLT1; a computational exploration. Journal of Biomolecular Structure and Dynamics 2024, 42 (22) , 12537-12547. https://doi.org/10.1080/07391102.2023.2270708
    43. Lauro Ribeiro de Souza Neto, Bogar Omar Montoya, José Brandão-Neto, Anil Verma, Sebastian Bowyer, José Teófilo Moreira-Filho, Rafael Ferreira Dantas, Bruno Junior Neves, Carolina Horta Andrade, Frank von Delft, Raymond J. Owens, Nicholas Furnham, Floriano Paes Silva-Jr. Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni. Scientific Reports 2024, 14 (1) https://doi.org/10.1038/s41598-024-52018-2
    44. Lizeth Escamilla-García, Rosa M. Jiménez-Barrera, Horacio Reyes-Pérez, Julio Silva Mendoza, David Alejandro Hernández, E. Bojórquez-Quintal, Roberto Rodríguez-Ortiz, María C. García-López, Rodrigo Chan-Navarro. Rapid and selective detection of Gram-positive bacteria using new dual emissive and non-cytotoxic organoboron esters. Dyes and Pigments 2024, 231 , 112395. https://doi.org/10.1016/j.dyepig.2024.112395
    45. Vineeta Pandey, Aarshi Srivastava, Nupur Singh, Ramwant Gupta, Akhtar Ali, R. K. Gaur. In-silico prediction of domain involved in chilli protein interaction with chilli leaf curl virus and associated betasatellite encoded protein. Discover Plants 2024, 1 (1) https://doi.org/10.1007/s44372-024-00016-z
    46. Franklyn Nonso Iheagwam, Gloria Aniedi Itina, Oyinkansola Ayobolanle Faluyi, Mercy Bella-Omunagbe, Samuel Akpoyowvare Ejoh. Anti-Obesity Potential of Secamone afzelii K. Leaf and Vine Ethanol Extract: Insights into Lipase Inhibition and Secondary Metabolites. Sci 2024, 6 (4) , 70. https://doi.org/10.3390/sci6040070
    47. Mazumder Adhish, I. Manjubala. Integrative in-silico and in-vitro analysis of taurine and vitamin B12 in modulating PPARγ and Wnt signaling in hyperhomocysteinemia-induced osteoporosis. Biology Direct 2024, 19 (1) https://doi.org/10.1186/s13062-024-00581-z
    48. Lars Binkle-Ladisch, Andy Pironet, Andrea Zaliani, Chantal Alcouffe, Daniel Mensching, Undine Haferkamp, Anne Willing, Marcel S. Woo, Alexandre Erdmann, Timm Jessen, Stephen D. Hess, Philip Gribbon, Ole Pless, Rudi Vennekens, Manuel A. Friese. Identification and development of TRPM4 antagonists to counteract neuronal excitotoxicity. iScience 2024, 27 (12) , 111425. https://doi.org/10.1016/j.isci.2024.111425
    49. Antti Pihlajamäki, María Francisca Matus, Sami Malola, Hannu Häkkinen. GraphBNC: Machine Learning‐Aided Prediction of Interactions Between Metal Nanoclusters and Blood Proteins. Advanced Materials 2024, 36 (47) https://doi.org/10.1002/adma.202407046
    50. Yang Liao, Zhangle Wei, Hangwei Xu, Zhichao Zhang, Feng Zhu. Unlocking precision medicine: Innovative strategies for druggable target identification and therapeutic enhancement. Precision Medication 2024, 1 (1) , 100002. https://doi.org/10.1016/j.prmedi.2024.10.002
    51. Lalit P. Dewalkar, Swapnil K. Dahule, Sursh C. Masram. Triticum aestivum Octacosanol, a Potential Inhibitor of PCSK9 in Fat Diet–Induced Hypercholesteromia. Revista Brasileira de Farmacognosia 2024, 34 (5) , 1032-1043. https://doi.org/10.1007/s43450-024-00544-5
    52. Liang Chen, Dai Lu, Yuxi Wan, Yaqian Zou, Ruiyi Zhang, Tao Zhou, Bin Long, Kangming Zhu, Wei Wang, Xing Tian. Metabolite Profiling and Identification of Sweet/Bitter Taste Compounds in the Growth of Cyclocarya Paliurus Leaves Using Multiplatform Metabolomics. Foods 2024, 13 (19) , 3089. https://doi.org/10.3390/foods13193089
    53. Manuel Alejandro Hernández-Serda, Víctor H. Vázquez-Valadez, Pablo Aguirre-Vidal, Nathan M. Markarian, José L. Medina-Franco, Luis Alfonso Cardenas-Granados, Aldo Yoshio Alarcón-López, Pablo A. Martínez-Soriano, Ana María Velázquez-Sánchez, Rodolfo E. Falfán-Valencia, Enrique Angeles, Levon Abrahamyan. In Silico Identification of Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro). Pathogens 2024, 13 (10) , 887. https://doi.org/10.3390/pathogens13100887
    54. Sabita Rangra, Kamal Krishan Aggarwal. Characterization and kinetics of a cathepsin B-inhibiting protein from Musa acuminata Colla peel. Biochimie 2024, 29 https://doi.org/10.1016/j.biochi.2024.10.016
    55. Eduarda Guimarães Sousa, Andrei Giacchetto Felice, Fabiana Vieira Dominici, Arun Kumar Jaiswal, Mariana Letícia Costa Pedrosa, Luiza Pereira Reis, Lucas Gabriel Rodrigues Gomes, Vasco Ariston de Carvalho Azevedo, Siomar de Castro Soares. Unveiling Resistance and Virulence Mechanisms under Darwinian Positive Selection for Novel Drug Discovery for Gardnerella vaginalis. Venereology 2024, 3 (3) , 120-135. https://doi.org/10.3390/venereology3030010
    56. Yuyan Li, Qianwen Wu, Lingyi Zhu, Ruili Zhang, Boqiang Tong, Yan Wang, Yi Han, Yizeng Lu, Dequan Dou, Zhihui Tian, Jian Zheng, Yan Zhang. Heat-shock transcription factor HsfA8a regulates heat stress response in Sorbus pohuashanensis. Planta 2024, 260 (3) https://doi.org/10.1007/s00425-024-04486-z
    57. Grace M. Bennett, Julia Starczewski, Mark Vincent C. dela Cerna. In silico identification of putative druggable pockets in PRL3, a significant oncology target. Biochemistry and Biophysics Reports 2024, 39 , 101767. https://doi.org/10.1016/j.bbrep.2024.101767
    58. Cheng-Rui Zhang, Dai-Yan Zhang, Jin Gao, Zhi-Ming Cao, Yuan-Jia Hu. Exploring the mechanisms of Yuanhu Zhitong oral liquid for primary dysmenorrhea through network pharmacology, molecular docking, and molecular dynamics simulation. Reproductive and Developmental Medicine 2024, 8 (3) , 138-150. https://doi.org/10.1097/RD9.0000000000000097
    59. Diana Martínez-Valencia, Cecilia Bañuelos, Guillermina García-Rivera, Daniel Talamás-Lara, Esther Orozco, . The Entamoeba histolytica Vps26 (EhVps26) retromeric protein is involved in phagocytosis: Bioinformatic and experimental approaches. PLOS ONE 2024, 19 (8) , e0304842. https://doi.org/10.1371/journal.pone.0304842
    60. Dandan Feng, Congcong Yan, Longbin Yuan, Yuewen Jia, Yuying Sun, Jiquan Zhang. Genome-wide identification of crustacyanin and function analysis of one isoform high-expression in carapace from Neocaridina denticulata sinensis. International Journal of Biological Macromolecules 2024, 12 , 135070. https://doi.org/10.1016/j.ijbiomac.2024.135070
    61. Yassir Boulaamane, Kailash Jangid, Mohammed Reda Britel, Amal Maurady. Probing the molecular mechanisms of α-synuclein inhibitors unveils promising natural candidates through machine-learning QSAR, pharmacophore modeling, and molecular dynamics simulations. Molecular Diversity 2024, 28 (4) , 2495-2511. https://doi.org/10.1007/s11030-023-10691-x
    62. Abdullahi Tunde Aborode, Neeraj Kumar, Christopher Busayo Olowosoke, Tope Abraham Ibisanmi, Islamiyyah Ayoade, Haruna Isiyaku Umar, Abdullahi Temitope Jamiu, Basit Bolarinwa, Zainab Olapade, Abidemi Ruth Idowu, Ibrahim O. Adelakun, Isreal Ayobami Onifade, Benjamin Akangbe, Modesta Abacheng, Odion O. Ikhimiukor, Aeshah A. Awaji, Ridwan Olamilekan Adesola. Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences. Frontiers in Bioinformatics 2024, 4 https://doi.org/10.3389/fbinf.2024.1411935
    63. Meng Yu, Zhongqi Shen, Shaozhi Zhang, Yang Zhang, Hongwei Zhao, Longfei Zhang. The active components of Erzhi wan and their anti-Alzheimer's disease mechanisms determined by an integrative approach of network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulation. Heliyon 2024, 10 (13) , e33761. https://doi.org/10.1016/j.heliyon.2024.e33761
    64. Jose Luis Gonzalez-Llerena, Bryan Alejandro Espinosa-Rodriguez, Daniela Treviño-Almaguer, Luis Fernando Mendez-Lopez, Pilar Carranza-Rosales, Patricia Gonzalez-Barranco, Nancy Elena Guzman-Delgado, Antonio Romo-Mancillas, Isaias Balderas-Renteria. Cordycepin Triphosphate as a Potential Modulator of Cellular Plasticity in Cancer via cAMP-Dependent Pathways: An In Silico Approach. International Journal of Molecular Sciences 2024, 25 (11) , 5692. https://doi.org/10.3390/ijms25115692
    65. Dongying Zhang, Qixing Zhou, Zhen Zhang, Xiangxuan Yang, Jiaxu Man, Dongxue Wang, Xiaoyong Li. Based on Network Pharmacology and Molecular Docking, the Active Components, Targets, and Mechanisms of Flemingia philippinensis in Improving Inflammation Were Excavated. Nutrients 2024, 16 (12) , 1850. https://doi.org/10.3390/nu16121850
    66. Zi-Yong Chu, Xue-Jiao Zi. Network pharmacology, single gene survival analysis and molecular docking to study the mechanism of Sotetsuflavone in the treatment of pancreatic cancer. 2024https://doi.org/10.1101/2024.04.30.580419
    67. Kejue Wu, Yinfeng Guo, Tiefeng Xu, Weifeng Huang, Deyin Guo, Liu Cao, Jinping Lei. Structure-Based Virtual Screening for Methyltransferase Inhibitors of SARS-CoV-2 nsp14 and nsp16. Molecules 2024, 29 (10) , 2312. https://doi.org/10.3390/molecules29102312
    68. Alexandra M. Wiley, Jade Yang, Rivcka Madhani, Abhinav Nath, Rheem A. Totah. Investigating the association between CYP2J2 inhibitors and QT prolongation: a literature review. Drug Metabolism Reviews 2024, 56 (2) , 145-163. https://doi.org/10.1080/03602532.2024.2329928
    69. Hongkang Chu, Taigang Liu. Comprehensive Research on Druggable Proteins: From PSSM to Pre-Trained Language Models. International Journal of Molecular Sciences 2024, 25 (8) , 4507. https://doi.org/10.3390/ijms25084507
    70. Xinxin Zhao, Wenyu Wang, Xiaoli Zeng, Rong Xu, Bing Yuan, Wenyao Yu, Mingshu Wang, Renyong Jia, Shun Chen, Dekang Zhu, Mafeng Liu, Qiao Yang, Ying Wu, Shaqiu Zhang, Juan Huang, Xumin Ou, Di Sun, Anchun Cheng. Klebicin E, a pore-forming bacteriocin of Klebsiella pneumoniae, exploits the porin OmpC and the Ton system for translocation. Journal of Biological Chemistry 2024, 300 (3) , 105694. https://doi.org/10.1016/j.jbc.2024.105694
    71. Zi-Yong Chu, Xue-Jiao Zi. Network pharmacology, single gene survival analysis and molecular docking to study the mechanism of Sotetsuflavone in the treatment of pancreatic cancer. Pharmacological Research - Reports 2024, 2 , 100010. https://doi.org/10.1016/j.prerep.2024.100010
    72. Eduardo Burgos-Valencia, Ileana Echevarría-Machado, Gustavo Ortega-Lule, Fátima Medina-Lara, Federico García-Laynes, Manuel Martínez-Estévez, José Narváez-Zapata. Haplotype analysis, regulatory elements and docking simulation of structural models of different AT3 copies in the genus Capsicum. Journal of Biomolecular Structure and Dynamics 2024, 3 , 1-14. https://doi.org/10.1080/07391102.2024.2317991
    73. Ghanshyam Teli, Rohit Pal, Lalmohan Maji, Gurubasavaraja Swamy Purawarga Matada, Sindhuja Sengupta. Explanatory review on pyrimidine/fused pyrimidine derivatives as anticancer agents targeting Src kinase. Journal of Biomolecular Structure and Dynamics 2024, 42 (3) , 1582-1614. https://doi.org/10.1080/07391102.2023.2205943
    74. Atul Kumar Jaiswal, Prem Pratap Singh, Bhanu Prakash. Prospects of Bioinformatics and Data Acquirement Tools in Boosting the Application of Phytochemicals in Food Sciences. 2024, 281-302. https://doi.org/10.1007/978-981-99-4370-8_13
    75. Aluísio Marques da Fonseca, Neidelenio Baltazar Soares, Regilany Paulo Colares, Mauro Macedo de Oliveira, Larissa Santos Oliveira, Gabrielle Silva Marinho, Mira Raya Paula de Lima, Matheus Nunes da Rocha, Hélcio Silva dos Santos, Emmanuel Silva Marinho. Naphthoquinones biflorin and bis-biflorin ( Capraria biflora ) as possible inhibitors of the fungus Candida auris polymerase: molecular docking, molecular dynamics, MM/GBSA calculations and in silico drug-likeness study. Journal of Biomolecular Structure and Dynamics 2023, 41 (21) , 11564-11577. https://doi.org/10.1080/07391102.2022.2163702
    76. E. Gayozo, C. D. J. Arce. Evaluación y detección bioinformática de terpenoides con potencial inhibitorio de la proteína viral 1 (VP1) del virus de la bursitis infecciosa. Revista de la Facultad de Medicina Veterinaria y de Zootecnia 2023, 70 (3) , e106011. https://doi.org/10.15446/rfmvz.v70n3.106011
    77. Jina Kim, Eun Joo Kim, Hye-Jeong Ko, Yeon-Hee Lee, Soon-Kwang Hong, Miyoung Shin, Je Hyeon Lee, Woori Kwak. Construction of Streptomyces coelicolor A3(2) mutants that exclusively produce NA4/NA6 intermediates of agarose metabolism through mutation induction. Scientific Reports 2023, 13 (1) https://doi.org/10.1038/s41598-023-46410-7
    78. Chunye Zhang, Jiazheng Liu, Yuxiang Sui, Shuai Liu, Ming Yang. In silico drug repurposing carvedilol and its metabolites against SARS-CoV-2 infection using molecular docking and molecular dynamic simulation approaches. Scientific Reports 2023, 13 (1) https://doi.org/10.1038/s41598-023-48398-6
    79. Estefany Bello-Vargas, Mario Alberto Leyva-Peralta, Zeferino Gómez-Sandoval, Mario Ordóñez, Rodrigo Said Razo-Hernández. A Computational Method for the Binding Mode Prediction of COX-1 and COX-2 Inhibitors: Analyzing the Union of Coxibs, Oxicams, Propionic and Acetic Acids. Pharmaceuticals 2023, 16 (12) , 1688. https://doi.org/10.3390/ph16121688
    80. Vera Pfanzagl, Clemens Gruber-Grünwald, Urban Leitgeb, Paul G. Furtmüller, Christian Obinger. Posttranslational modification and heme cavity architecture of human eosinophil peroxidase—insights from first crystal structure and biochemical characterization. Journal of Biological Chemistry 2023, 299 (12) , 105402. https://doi.org/10.1016/j.jbc.2023.105402
    81. Daniel Mora, Frederick Schosinsky, Josue Castellón, Kevin González, Jaume Bastida, Silvana Pinheiro, William Zamora. Finding for New Drugs in Nature for Neglected Tropical Diseases: In Silico Study of Homolycorine Alkaloids Against Chagas Disease. 2023, 1-7. https://doi.org/10.1109/BIP60195.2023.10379389
    82. Henni‐Karoliina Ropponen, Eleonora Diamanti, Sandra Johannsen, Boris Illarionov, Rawia Hamid, Miriam Jaki, Peter Sass, Markus Fischer, Jörg Haupenthal, Anna K. H. Hirsch. Exploring the Translational Gap of a Novel Class of Escherichia coli IspE Inhibitors. ChemMedChem 2023, 18 (19) https://doi.org/10.1002/cmdc.202300346
    83. Ali Lillian Fox, Alyssa R. Teteris, Irimpan I. Mathews. Remote laboratory training for high school students: grocery store based hands-on project in protein crystallography. Journal of Applied Crystallography 2023, 56 (5) , 1557-1568. https://doi.org/10.1107/S1600576723006805
    84. Ghanshyam Teli, Rohit Pal, Lalmohan Maji, Sindhuja Sengupta, Nulgumnalli Manjunathaiah Raghavendra, Gurubasavaraja Swamy Purawarga Matada. Medicinal Chemistry Perspectives on Recent Advances in Src Kinase Inhibitors as a Potential Target for the Development of Anticancer Agents: Biological Profile, Selectivity, Structure‐Activity Relationship. Chemistry & Biodiversity 2023, 20 (9) https://doi.org/10.1002/cbdv.202300515
    85. Francesco Di Palma, Carlo Abate, Sergio Decherchi, Andrea Cavalli. Ligandability and druggability assessment via machine learning. WIREs Computational Molecular Science 2023, 13 (5) https://doi.org/10.1002/wcms.1676
    86. Rui Qiao, Wanggang Tang, Jiayan Li, Chen Li, Chaoyue Zhao, Xun Wang, Minghui Li, Yuchen Cui, Yanjia Chen, Guonan Cai, Qingyu Wu, Xiaoyu Zhao, Pengfei Wang. Structure-based virtual screening of ROCK1 inhibitors for the discovery of Enterovirus-A71 antivirals. Virology 2023, 585 , 205-214. https://doi.org/10.1016/j.virol.2023.06.011
    87. Mohamed Shafana Farveen, Thirumurthy Madhavan, Rajnish Narayanan. Association of Laccase from Bacillus cereus O2-B and Pseudomonas aeruginosa O1-P with the bio-degradation of polymers: an in vitro to in silico approach. Biodegradation 2023, 34 (4) , 383-403. https://doi.org/10.1007/s10532-023-10028-3
    88. N. V. Khmil, V. G. Kolesnikov. Molecular docking of human serum albumin with penicillin G determinants. Biophysical Bulletin 2023, (49) , 7-19. https://doi.org/10.26565/2075-3810-2023-49-01
    89. Aluísio Marques da Fonseca, Neidelênio Baltazar Soares, Maria Imaculada Lourenço Meirú, Regilany Paulo Colares, Moises Maia Neto, Antonio Carlos Nogueira Sobrinho, Hélcio Silva dos Santos, Emmanuel Silva Marinho. Combined study of docking and molecular dynamics against DNV-3 SN1 protein by bixinoids. Journal of Biomolecular Structure and Dynamics 2023, 41 (10) , 4549-4559. https://doi.org/10.1080/07391102.2022.2070282
    90. Nikolas Hörmann, Christina Kalchschmid, Patricia Grabher, Isabella Grassmayr, Paul Kapitza, Teresa Kaserer, Ronald Gust. Development of heterodimeric estrogen receptor alpha antagonists to target simultaneously the ligand and coactivator binding site. Archiv der Pharmazie 2023, 356 (7) https://doi.org/10.1002/ardp.202200638
    91. Shivananda Kandagalla, Bhimanagoud Kumbar, Jurica Novak. Structural Modifications Introduced by NS2B Cofactor Binding to the NS3 Protease of the Kyasanur Forest Disease Virus. International Journal of Molecular Sciences 2023, 24 (13) , 10907. https://doi.org/10.3390/ijms241310907
    92. Maitri Bhatt, Pravin Shende. Advancement in Machine Learning: A Strategic Lookout from Cancer Identification to Treatment. Archives of Computational Methods in Engineering 2023, 30 (4) , 2777-2792. https://doi.org/10.1007/s11831-023-09886-0
    93. David J. Pérez, Rodrigo S. Razo-Hernández, Miguel A. Ávila-Rodríguez. In silico Study on the Binding Interactions of SSTA and 18F-SSTA Towards Somatostatin Receptor Subtype 2. Anti-Cancer Agents in Medicinal Chemistry 2023, 23 (9) , 1048-1066. https://doi.org/10.2174/1871520623666230104160635
    94. Oluwamayowa Joshua Ogun, Georg Thaller, Doreen Becker. Molecular Structural Analysis of Porcine CMAH–Native Ligand Complex and High Throughput Virtual Screening to Identify Novel Inhibitors. Pathogens 2023, 12 (5) , 684. https://doi.org/10.3390/pathogens12050684
    95. Qinjie Xiao, Yumin Feng, Li Chen, Mu Li, Pengfei Zhang, Qiuyan Wang, Anming Wang, Xiaolin Pei. Engineered aldoxime dehydratase to enable the chemoenzymatic conversion of benzyl amines to aromatic nitriles. Bioorganic Chemistry 2023, 134 , 106468. https://doi.org/10.1016/j.bioorg.2023.106468
    96. Robert A. Zimmermann, Tim R. Fischer, Marvin Schwickert, Zarina Nidoieva, Tanja Schirmeister, Christian Kersten. Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6. International Journal of Molecular Sciences 2023, 24 (7) , 6109. https://doi.org/10.3390/ijms24076109
    97. Duncan Allardyce, Priscilla Adu Mantey, Monika Szalecka, Robert Nkwo, Eriketi Z. Loizidou. Identification of a new class of proteasome inhibitors based on a naphthyl–azotricyclic-urea–phenyl scaffold. RSC Medicinal Chemistry 2023, 14 (3) , 573-582. https://doi.org/10.1039/D2MD00404F
    98. Mark Reglinski, Laura Monlezun, Sarah J. Coulthurst. The accessory protein TagV is required for full Type VI secretion system activity in Serratia marcescens. Molecular Microbiology 2023, 119 (3) , 326-339. https://doi.org/10.1111/mmi.15027
    99. Eva-Maria Zangerl-Plessl, Wei Wu, Michael C. Sanguinetti, Anna Stary-Weinzinger. Binding of RPR260243 at the intracellular side of the hERG1 channel pore domain slows closure of the helix bundle crossing gate. Frontiers in Molecular Biosciences 2023, 10 https://doi.org/10.3389/fmolb.2023.1137368
    100. Soumyadip Chakrobarty, Swarnava Garai, Arabinda Ghosh, Nobendu Mukerjee, Deeplina Das. Bioactive plantaricins as potent anti-cancer drug candidates: double docking, molecular dynamics simulation and in vitro cytotoxicity analysis. Journal of Biomolecular Structure and Dynamics 2023, 27 , 1-11. https://doi.org/10.1080/07391102.2023.2177732
    Load more citations
    Download PDF
    Go to Journal of Chemical Information and Modeling
    Get e-Alerts
    Get e-Alerts

    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2012, 52, 2, 360–372
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ci200454v
    Published December 8, 2011
    Copyright © 2011 American Chemical Society
    Request reuse permissions

    Article Views

    4926

    Altmetric

    -

    Citations

    332
    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.