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FRED Pose Prediction and Virtual Screening Accuracy

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OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States
Cite this: J. Chem. Inf. Model. 2011, 51, 3, 578–596
Publication Date (Web):February 16, 2011
Copyright © 2011 American Chemical Society

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    Results of a previous docking study are reanalyzed and extended to include results from the docking program FRED and a detailed statistical analysis of both structure reproduction and virtual screening results. FRED is run both in a traditional docking mode and in a hybrid mode that makes use of the structure of a bound ligand in addition to the protein structure to screen molecules. This analysis shows that most docking programs are effective overall but highly inconsistent, tending to do well on one system and poorly on the next. Comparing methods, the difference in mean performance on DUD is found to be statistically significant (95% confidence) 61% of the time when using a global enrichment metric (AUC). Early enrichment metrics are found to have relatively poor statistical power, with 0.5% early enrichment only able to distinguish methods to 95% confidence 14% of the time.

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    A complete set of figures and tables for early enrichment results, a list of the OMEGA and FRED options used for each mode, and more. This material is available free of charge via the Internet at

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    75. G. Madhavi Sastry, V. S. Sandeep Inakollu, and Woody Sherman . Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking. Journal of Chemical Information and Modeling 2013, 53 (7) , 1531-1542.
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    77. Tanja Schulz-Gasch, Christin Schärfer, Wolfgang Guba, and Matthias Rarey . TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations. Journal of Chemical Information and Modeling 2012, 52 (6) , 1499-1512.
    78. Enrico O. Purisima and Hervé Hogues . Protein–Ligand Binding Free Energies from Exhaustive Docking. The Journal of Physical Chemistry B 2012, 116 (23) , 6872-6879.
    79. Marcel L. Verdonk, Ilenia Giangreco, Richard J. Hall, Oliver Korb, Paul N. Mortenson, and Christopher W. Murray . Docking Performance of Fragments and Druglike Compounds. Journal of Medicinal Chemistry 2011, 54 (15) , 5422-5431.
    80. Grégory Menchon, Laurent Maveyraud, Georges Czaplicki. Molecular Dynamics as a Tool for Virtual Ligand Screening. 2024, 33-83.
    81. Mostafa M. M. El-Miligy, Marwa E. Abdelaziz, Salwa M. Fahmy, Tamer M. Ibrahim, Marwa M. Abu-Serie, Mona A. Mahran, Aly A. Hazzaa. Discovery of new pyridine-quinoline hybrids as competitive and non-competitive PIM-1 kinase inhibitors with apoptosis induction and caspase 3/7 activation capabilities. Journal of Enzyme Inhibition and Medicinal Chemistry 2023, 38 (1)
    82. Matthew F. D. Hurley, Robert M. Raddi, Jason G. Pattis, Vincent A. Voelz. Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host–guest challenge. Physical Chemistry Chemical Physics 2023, 25 (47) , 32393-32406.
    83. Kosaku Okuda, Kengo Nakahara, Akihiro Ito, Yuta Iijima, Ryosuke Nomura, Ashutosh Kumar, Kana Fujikawa, Kazuya Adachi, Yuki Shimada, Satoshi Fujio, Reina Yamamoto, Nobumasa Takasugi, Kunishige Onuma, Mitsuhiko Osaki, Futoshi Okada, Taichi Ukegawa, Yasuo Takeuchi, Norihisa Yasui, Atsuko Yamashita, Hiroyuki Marusawa, Yosuke Matsushita, Toyomasa Katagiri, Takahiro Shibata, Koji Uchida, Sheng-Yong Niu, Nhi B. Lang, Tomohiro Nakamura, Kam Y. J. Zhang, Stuart A. Lipton, Takashi Uehara. Pivotal role for S-nitrosylation of DNA methyltransferase 3B in epigenetic regulation of tumorigenesis. Nature Communications 2023, 14 (1)
    84. Simone Albani, Ivan Polsinelli, Luca Mazzei, Francesco Musiani, Stefano Benini. Determination and Kinetic Characterization of a New Potential Inhibitor for AmsI Protein Tyrosine Phosphatase from the Apple Pathogen Erwinia amylovora. Molecules 2023, 28 (23) , 7774.
    85. Tuomas Pylkkö, Tihomir Tomašič, Antti Poso, Päivi Tammela. Virtual Screening Assisted Search for Inhibitors of the Translocated Intimin Receptor of Enteropathogenic Escherichia Coli. ChemBioChem 2023,
    86. Manokaran Malini, Ramasamy Thilagavathi, Jannet Vennila, Beutline Malgija, Gandhi Praveena, Chelliah Selvam. Identification of small-molecule glucokinase activator for type-2-diabetes treatment: a structure-based virtual screening approach. Molecular Simulation 2023, 49 (17) , 1596-1613.
    87. Deborah Quaglio, Paola Infante, Silvia Cammarone, Lara Lamelza, Marilisa Conenna, Francesca Ghirga, Gennaro Adabbo, Luca Pisano, Lucia Di Marcotullio, Bruno Botta, Mattia Mori. Exploring the Potential of Anthraquinone‐Based Hybrids for Identifying a Novel Generation of Antagonists for the Smoothened Receptor in HH‐Dependent Tumour. Chemistry – A European Journal 2023, 29 (62)
    88. Yang Hou, Yuqian Bai, Chang Lu, Qiuchan Wang, Zishi Wang, Jinsheng Gao, Hongliang Xu. Applying molecular docking to pesticides. Pest Management Science 2023, 79 (11) , 4140-4152.
    89. Daniela Istrate, Luminita Crisan. Dipeptidyl Peptidase 4 Inhibitors in Type 2 Diabetes Mellitus Management: Pharmacophore Virtual Screening, Molecular Docking, Pharmacokinetic Evaluations, and Conceptual DFT Analysis. Processes 2023, 11 (11) , 3100.
    90. Jacqueline Kuan, Mariia Radaeva, Adeline Avenido, Artem Cherkasov, Francesco Gentile. Keeping pace with the explosive growth of chemical libraries with structure‐based virtual screening. WIREs Computational Molecular Science 2023, 13 (6)
    91. Rupali S. Prasad, Rupesh V. Chikhale, Nitish Rai, Natasha S. Akojwar, Raksha A. Purohit, Pravesh Sharma, Onkar Kulkarni, Damiki Laloo, Shailendra S. Gurav, Prakash R. Itankar, Satyendra K. Prasad. Rutin from Begonia roxburghii modulates iNOS and Sep A activity in treatment of Shigella flexneri induced diarrhoea in rats: An in vitro, in vivo and computational analysis. Microbial Pathogenesis 2023, 184 , 106380.
    92. Mayar Tarek Ibrahim, Peng Tao. Computational investigation of peptidomimetics as potential inhibitors of SARS-CoV-2 spike protein. Journal of Biomolecular Structure and Dynamics 2023, 41 (15) , 7144-7157.
    93. Mariana Sant’Anna Pereira Nicolau, Milllena Almeida Resende, Pedro Serafim, Germano Yoneda Pereira Lima, Carlos Ueira-Vieira, Nilson Nicolau-Junior, Kelly Aparecida Geraldo Yoneyama. Identification of potential inhibitors for N-myristoyltransferase (NMT) protein of Plasmodium vivax. Journal of Biomolecular Structure and Dynamics 2023, 41 (15) , 7019-7031.
    94. Laura Raniere Borges dos Anjos, Vinícius Alexandre Fiaia Costa, Bruno Junior Neves, Ana Paula Junqueira-Kipnis, André Kipnis. Repurposing miconazole and tamoxifen for the treatment of Mycobacterium abscessus complex infections through in silico chemogenomics approach. World Journal of Microbiology and Biotechnology 2023, 39 (10)
    95. Nace Zidar, Tihomir Tomašič, Danijel Kikelj, Martina Durcik, Jan Tytgat, Steve Peigneur, Marc Rogers, Alexander Haworth, Robert W. Kirby. New aryl and acylsulfonamides as state-dependent inhibitors of Nav1.3 voltage-gated sodium channel. European Journal of Medicinal Chemistry 2023, 258 , 115530.
    96. Dakshinamurthy Sivakumar, Sangwook Wu. Structural Bioinformatics and Artificial Intelligence Approaches in De Novo Drug Design. 2023, 44-61.
    97. Sarah Naomi Bolz, Michael Schroeder. Promiscuity in drug discovery on the verge of the structural revolution: recent advances and future chances. Expert Opinion on Drug Discovery 2023, 18 (9) , 973-985.
    98. Mohammed Nooraldeen Mahmod Al-Qattan, Mohd Nizam Mordi. Development and application of fragment-based de novo inhibitor design approaches against Plasmodium falciparum GST. Journal of Molecular Modeling 2023, 29 (9)
    99. Tamer M. Ibrahim, Ghada Abada, Marcel Dammann, Raed M. Maklad, Wagdy M. Eldehna, Rofaida Salem, Marwa M. Abdelaziz, Ramadan A. El-domany, Adnan A. Bekhit, Frank M. Beockler. Tetrahydrobenzo[h]quinoline derivatives as a novel chemotype for dual antileishmanial-antimalarial activity graced with antitubercular activity: Design, synthesis and biological evaluation. European Journal of Medicinal Chemistry 2023, 257 , 115534.
    100. Nikola Nedeljkovic, Vladimir Dobricic, Marina Mijajlovic, Zorica Vujic, Milos Nikolic. Molecular Docking Analysis of Novel Thiourea Derivatives of Naproxen with Potential Antitumor Activity. Experimental and Applied Biomedical Research (EABR) 2023, 24 (3) , 235-242.
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