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  1. 1.   Distinct allosteric networks in CDK4 and CDK6 in the cell cycle and in drug resistance
  2. Zhang,Wengang; Bradburn, Devin; Heidebrink, Gretchen; Liu, Yonglan; Jang,Hyunbum; Nussinov,Ruth; Kõivomägi, Mardo
  3. Journal of Molecular Biology. 2025, Mar 31; 169121.
  1. 2.   ShiftScan: A tool for rapid analysis of high-throughput differential scanning fluorimetry data and compound prioritization
  2. Waterworth, Samantha C; Shenoy, Shilpa R; Sharma, Nirmala D; Wolcott,Chris; Donohue,Duncan; O'Keefe,Barry; Beutler,John
  3. Protein Science : a publication of the Protein Society. 2025, Mar; 34(3): e70055.
  1. 3.   Multi-objective latent space optimization of generative molecular design models
  2. Abeer, A N M Nafiz; Urban, Nathan M; Weil,Michael; Alexander, Francis J; Yoon, Byung-Jun
  3. Patterns (New York, N.Y.). 2024, Oct 11; 5(10): 101042.
  1. 4.   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. 5.   Slower CDK4 and faster CDK2 activation in the cell cycle
  2. Zhang,Wengang; Liu,Yonglan; Jang,Hyunbum; Nussinov,Ruth
  3. Structure (London, England : 1993). 2024, Apr 23;
  1. 6.   A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening
  2. Vasanthakumari, Priyanka; Zhu, Yitan; Brettin, Thomas; Partin, Alexander; Shukla, Maulik; Xia, Fangfang; Narykov, Oleksandr; Weil,Michael; Stevens, Rick L
  3. Cancers. 2024, Jan 26; 16(3):
  1. 7.   Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction
  2. Fan, Ya Ju; Allen, Jonathan E; McLoughlin, Kevin S; Shi, Da; Bennion, Brian J; Zhang, Xiaohua; Lightstone, Felice C
  3. Artificial Intelligence Chemistry. 2023, Jun; 1(1):
  1. 8.   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. 9.   Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design
  2. Shaw,Gary; Fan,Lixin; Cherry,Scott; Shi,Genbin; Tropea, Joseph E; Ji,Xinhua
  3. Current Research in Structural Biology. 2023, Jan 30; 5: 100095.
  1. 10.   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. 11.   Target 2035-update on the quest for a probe for every protein
  2. Mueller, Susanne; Ackloo, Suzanne; Al Chawaf, Arij; Al-Lazikani, Bissan; Antolin, Albert; Baell, Jonathan B.; Beck, Hartmut; Beedie, Shaunna; Betz, Ulrich A. K.; Bezerra, Gustavo Arruda; Brennan, Paul E.; Brown, David; Brown, Peter J.; Bullock, Alex N.; Carter, Adrian J.; Chaikuad, Apirat; Chaineau, Mathilde; Ciulli, Alessio; Collins, Ian; Dreher, Jan; Drewry, David; Edfeldt, Kristina; Edwards, Aled M.; Egner, Ursula; Frye, Stephen; Fuchs, Stephen M.; Hall, Matthew D.; Hartung, Ingo; Hillisch, Alexander; Hitchcock, Stephen H.; Homan, Evert; Kannan, Natarajan; Kiefer, James R.; Knapp, Stefan; Kostic, Milka; Kubicek, Stefan; Leach, Andrew R.; Lindemann, Sven; Marsden, Brian D.; Matsui, Hisanori; Meier,Jordan; Merk, Daniel; Michel, Maurice; Morgan, Maxwell R.; Mueller-Fahrnow, Anke; Owen, Dafydd R.; Perry, Benjamin G.; Rosenberg, Saul H.; Saikatendu, Kumar Singh; Schapira, Matthieu; Scholten, Cora; Sharma, Sujata; Simeonov, Anton; Sundstrom, Michael; Superti-Furga, Giulio; Todd, Matthew H.; Tredup, Claudia; Vedadi, Masoud; von Delft, Frank; Willson, Timothy M.; Winter, Georg E.; Workman, Paul; Arrowsmith, Cheryl H.
  3. RSC Medicinal Chemistry . 2022, Jan 27; 13(1): 13-21.
  1. 12.   Mechanism of activation and the rewired network: New drug design concepts
  2. Nussinov,Ruth; Zhang,Mingzhen; Maloney, Ryan; Tsai,Chung-Jung; Yavuz, Bengi Ruken; Tuncbag, Nurcan; Jang, Hyunbum
  3. Medicinal research reviews. 2021, Oct 25; 0198-6325:
  1. 13.   Drugging multiple same-allele driver mutations in cancer
  2. Nussinov,Ruth; Zhang,Mingzhen; Maloney,Ryan; Jang, Hyunbum
  3. Expert Opinion on Drug Discovery. 2021, Aug; 16(8): 823-828.
  1. 14.   MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization
  2. Cai, Tian; Lim, Hansaim; Abbu, Kyra Alyssa; Qiu, Yue; Nussinov,Ruth; Xie, Lei
  3. Journal of Chemical Information and Modeling. 2021, Apr 26; 61(4): 1570-1582.
  1. 15.   Crystallographic models of SARS-CoV-2 3CL(pro): in-death assessment of structure quality and validation
  2. Jaskolski, Mariusz; Dauter, Zbigniew; Shabalin, Ivan G.; Gilski, Miroslaw; Brzezinski, Dariusz; Kowiel, Marcin; Rupp, Bernhard; Wlodawer,Alexander
  3. IUCrJ. 2021, Feb 9; 8(Pt 2): 238-256.
  1. 16.   Predicting Volume of Distribution in Humans: Performance of in silico Methods for A Large Set of Structurally Diverse Clinical Compounds
  2. Murad, Neha; Pasikanti, Kishore K; Madej,Benjamin; Minnich, Amanda; McComas, Juliet M; Crouch, Sabrinia; Polli, Joseph W; Weber, Andrew D
  3. Drug metabolism and disposition: the biological fate of chemicals. 2021, Feb 1; 49: 169-178.
  1. 17.   Deciphering the chemical instability of sphaeropsidin A under physiological conditions - degradation studies and structural elucidation of the major metabolite
  2. van der Westhuyzen, Alet E; Ingels, Aude; Rosière, Rémi; Amighi, Karim; Oberer, Lukas; Gustafson,Kirk; Wang,Dongdong; Evidente, Antonio; Maddau, Lucia; Masi, Marco; de Villiers, André; Green, Ivan R; Berger, Walter; Kornienko, Alexander; Mathieu, Veronique; van Otterlo, Willem A L
  3. Organic & biomolecular chemistry. 2020, OCT 28; 18(40): 8147-8160.
  1. 18.   Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models
  2. Brzezinski, Dariusz; Kowiel, Marcin; Cooper, David R; Cymborowski, Marcin; Grabowski, Marek; Wlodawer,Alexander; Dauter,Zbigniew; Shabalin, Ivan G; Gilski, Miroslaw; Rupp, Bernhard; Jaskolski, Mariusz; Minor, Wladek
  3. Protein science : a publication of the Protein Society. 2020, OCT 8;
  1. 19.   Creating and screening natural product libraries
  2. Wilson,Brice; Thornburg,Chris; Henrich,Curtis; Grkovic,Tanja; O'Keefe,Barry
  3. Natural product reports. 2020, JUL 1; 37: 893-918.
  1. 20.   Accelerating Therapeutics for Opportunities in Medicine: A Paradigm Shift in Drug Discovery
  2. Hinkson, Izumi V; Madej,Benjamin; Stahlberg,Eric
  3. Frontiers in pharmacology. 2020, Jun 30; 11: 770.
  1. 21.   Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank
  2. Wlodawer,Alexander; Dauter,Zbigniew; Shabalin, Ivan; Gilski, Miroslaw; Brzezinski, Dariusz; Kowiel, Marcin; Minor, Wladek; Rupp, Bernhard; Jaskolski, Mariusz
  3. The FEBS journal. 2020, JUN 24;
  1. 22.   Structural Fluidity of the Human Immunodeficiency Virus Rev Response Element
  2. Sherpa,Chringma; Le Grice,Stuart
  3. Viruses. 2020, Jan; 12(1):
  1. 23.   Natural Products as a Foundation for Drug Discovery
  2. Beutler,John
  3. Current protocols in pharmacology. 2019, Sep; 86(1): e67.
  1. 24.   Is Nanoclustering essential for all oncogenic KRas pathways? Can it explain why wild-type KRas can inhibit its oncogenic variant?
  2. Nussinov,Ruth; Tsai,Chung-Jung; Jang,Hyunbum
  3. Seminars in Cancer Biology. 2019, FEB; 54: 114-120.
  1. 25.   New weapons to penetrate the armor: Novel reagents and assays developed at the NCI RAS Initiative to enable discovery of RAS therapeutics
  2. Esposito,Dom; Stephen,Andy; Turbyville,Tommy; Holderfield, Matthew
  3. Seminars in Cancer Biology. 2019, Feb; 54: 174-182.
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