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  1. 1.   Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting
  2. Narykov, Oleksandr; Zhu, Yitan; Brettin, Thomas; Evrard,Yvonne; Partin, Alexander; Xia, Fangfang; Shukla, Maulik; Vasanthakumari, Priyanka; Doroshow, James H; Stevens, Rick L
  3. Briefings in Bioinformatics. 2025, Mar 04; 26(2):
  1. 2.   Correlation of protein binding pocket properties with hits' chemistries used in generation of ultra-large virtual libraries
  2. Song, Robert X; Nicklaus,Marc; Tarasova,Nadya
  3. Journal of Computer-Aided Molecular Design. 2024, May 16; 38(1): 22.
  1. 3.   DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking
  2. Balius,Trent; Tan, Y Stanley; Chakrabarti,Mayukh
  3. Journal of Computational Chemistry. 2023, Sep 25;
  1. 4.   Virtual Screening of Hepatitis B Virus Pre-Genomic RNA as a Novel Therapeutic Target
  2. Olenginski, Lukasz T; Kasprzak, Wojciech K; Attionu, Solomon K; Shapiro, Bruce A; Dayie, Theodore K
  3. Molecules (Basel, Switzerland). 2023, Feb 14; 28(4):
  1. 5.   Virtual screening for small-molecule pathway regulators by image-profile matching
  2. Rohban, Mohammad H; Fuller, Ashley M; Tan, Ceryl; Goldstein, Jonathan T; Syangtan, Deepsing; Gutnick, Amos; DeVine, Ann; Nijsure, Madhura P; Rigby,Megan; Sacher, Joshua R; Corsello, Steven M; Peppler, Grace B; Bogaczynska, Marta; Boghossian, Andrew; Ciotti, Gabrielle E; Hands, Allison T; Mekareeya, Aroonroj; Doan, Minh; Gale, Jennifer P; Derynck, Rik; Turbyville,Tommy; Boerckel, Joel D; Singh, Shantanu; Kiessling, Laura L; Schwarz, Thomas L; Varelas, Xaralabos; Wagner, Florence F; Kafri, Ran; Eisinger-Mathason, T S Karin; Carpenter, Anne E
  3. Cell Systems. 2022, Sep 01; 13(9): 724-736.e9.
  1. 6.   (Q)SAR Models of HIV-1 Protein Inhibition by Drug-Like Compounds
  2. Stolbov, Leonid A; Druzhilovskiy, Dmitry S; Filimonov, Dmitry A; Nicklaus,Marc; Poroikov, Vladimir V
  3. Molecules (Basel, Switzerland). 2020, Jan 1; 25(1):
  1. 7.   Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing
  2. Pogodin, P V; Lagunin, A A; Filimonov, D A; Nicklaus,Marc; Poroikov, V V
  3. SAR and QSAR in environmental research. 2019, OCT 3; 30(10): 759-773.
  1. 8.   How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors
  2. Pogodin, Pavel V; Lagunin, Alexey A; Rudik, Anastasia V; Filimonov, Dmitry A; Druzhilovskiy, Dmitry S; Nicklaus, Marc; Poroikov, Vladimir V
  3. Frontiers in chemistry. 2018, Apr 26; 6: 133.
  1. 9.   Software and resources for computational medicinal chemistry
  2. Liao, C. Z.; Sitzmann, M.; Pugliese, A.; Nicklaus, M. C.
  3. Future Medicinal Chemistry. 2011, Jun; 3(8): 1057-1085.
  1. 10.   Inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1) developed by virtual screening using ligand-based pharmacophores
  2. Weidlich, I. E.; Dexheimer, T.; March, C.; Antony, S.; Pommier, Y.; Nicklaus, M. C.
  3. Bioorganic & Medicinal Chemistry. 2010, Jan; 18(1): 182-189.
  1. 11.   Virtual screening application of a model of full-length HIV-1 integrase complexed with viral DNA
  2. Liao, C. Z.; Karki, R. G.; March, C.; Pommier, Y.; Nicklaus, M. C.
  3. Bioorganic & Medicinal Chemistry Letters. 2007, Oct; 17(19): 5361-5365.
  1. 12.   Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design
  2. Dror, O.; Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J.
  3. Current Medicinal Chemistry. 2004 11(1): 71-90.
  1. 13.   Virtual screening of ultra-large chemical libraries identifies cell-permeable small-molecule inhibitors of a "non-druggable" target, STAT3 N-terminal domain
  2. Andrade Bonilla,Pedro; Hoop,Cody; Stefanisko, Karen; Tarasov,Sergey; Sinha, Sourav; Nicklaus,Marc; Tarasova,Nadya
  3. Frontiers in Oncology. 2023 13: 1144153.
  1. 14.   Considerations Around Structure-Based Drug Discovery for KRAS Using DOCK
  2. Chakrabarti,Mayukh; Tan, Y Stanley; Balius,Trent
  3. Methods in Molecular Biology (Clifton, N.J.). 2024 2797: 67-90.
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