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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.   Radiation cataract in Heterogeneous Stock mice after gamma-ray or HZE ion exposure
  2. Kleiman, Norman J; Edmondson,Elijah; Weil, Michael M; Fallgren, Christina M; King, Adam; Schmidt, Catherine; Hall, Eric J
  3. Life Sciences in Space Research. 2024, Feb; 40: 97-105.
  1. 4.   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. 5.   Feasibility of a virtual reality intervention targeting distress and anxiety symptoms in patients with primary brain tumors: Interim analysis of a phase 2 clinical trial
  2. King, Amanda L; Roche, Kayla N; Leeper, Heather E; Vera, Elizabeth; Mendoza, Tito; Mentges, Kelly; Acquaye-Mallory, Alvina A; Adegbesan, Kendra A; Boris, Lisa; Burton, Eric; Choi, Anna; Grajkowska, Ewa; Kunst, Tricia; Levine, Jason; Lollo, Nicole; Miller, Hope; Panzer, Marissa; Penas-Prado, Marta; Pillai, Valentina; Polskin, Lily; Reyes, Jennifer; Sahebjam, Solmaz; Stockdill, Macy L; Theeler, Brett J; Wu, Jing; Gilbert, Mark R; Armstrong, Terri S
  3. Journal of Neuro-oncology. 2023, Mar 08; 1-9.
  1. 6.   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. 7.   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. 8.   (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. 9.   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. 10.   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. 11.   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. 12.   Enhanced Stereoselectivity of a Cu(II) Complex Chiral Auxiliary in the Synthesis of Fmoc-L-gamma-carboxyglutamic Acid
  2. Smith, D. J.; Yap, G. P. A.; Kelley, J. A.; Schneider, J. P.
  3. Journal of Organic Chemistry. 2011, Mar; 76(6): 1513-1520.
  1. 13.   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. 14.   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. 15.   Homology model of RSK2 N-terminal kinase domain, structure-based identification of novel RSK2 inhibitors, and preliminary common pharmacophore
  2. Nguyen, T. L.; Gussio, R.; Smith, J. A.; Lannigan, D. A.; Hecht, S. M.; Scudiero, D. A.; Shoemaker, R. H.; Zaharevitz, D. W.
  3. Bioorganic & Medicinal Chemistry. 2006, Sep; 14(17): 6097-6105.
  1. 16.   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. 17.   Looking for cancer clues in publicly accessible databases
  2. Medjahed, D.; Lemkin, P. F.; Smythers, G. W.; Munroe, D. J.
  3. Comparative and Functional Genomics. 2004 5(2): 196-200.
  1. 18.   Tissue Molecular Anatomy Project (TMAP): An expression database for comparative cancer proteomics
  2. Medjahed, D.; Luke, B. T.; Tontesh, T. S.; Smythers, G. W.; Munroe, D. J.; Lemkin, P. F.
  3. Proteomics. 2003 3(8): 1445-1453.
  1. 19.   VIRTUAL2D: A web-accessible predictive database for proteomics analysis
  2. Medjahed, D.; Smythers, G. W.; Powell, D. A.; Stephens, R. M.; Lemkin, P. F.; Munroe, D. J.
  3. Proteomics. 2003 3(2): 129-138.
  1. 20.   Exploring the immunomodulatory role of virtual memory CD8+ T cells: Role of IFN gamma in tumor growth control
  2. Savid-Frontera, Constanza; Viano, Maria Estefania; Baez, Natalia S; Lidon, Nicolas L; Fontaine, Quentin; Young,Howard; Vimeux, Lene; Donnadieu, Emmanuel; Rodriguez-Galan, Maria Cecilia
  3. Frontiers in Immunology. 2022 13: 971001.
  1. 21.   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. 22.   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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