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  1. 1.   Optimization of the PROTAC linker region of the proteasome substrate receptor hRpn13 rationalized structural modeling with molecular dynamics
  2. Lu,Xiuxiu; Sabbasani, Venkata R; Walters,Kylie; Swenson, Rolf E; Walters,Kylie
  3. The Journal of Biological Chemistry. 2025, Apr 18; 108520.
  1. 2.   Waterless structures in the Protein Data Bank
  2. Wlodawer,Alexander; Dauter, Zbigniew; Rubach, Pawel; Minor, Wladek; Loch, Joanna I; Brzezinski, Dariusz; Gilski, Miroslaw; Jaskolski, Mariusz
  3. IUCrJ. 2024, Nov 01;
  1. 3.   Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature
  2. Chen, Julian C H; Gilski, Miroslaw; Chang, Changsoo; Borek, Dominika; Rosenbaum, Gerd; Lavens, Alex; Otwinowski, Zbyszek; Kubicki, Maciej; Dauter, Zbigniew; Jaskolski, Mariusz; Joachimiak, Andrzej
  3. IUCrJ. 2024, Sep 01; 11(Pt 5): 649-663.
  1. 4.   Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures
  2. Hao,Ming; Imamichi,Tomozumi; Chang,Weizhong
  3. International Journal of Molecular Sciences. 2024, Feb 02; 25(3):
  1. 5.   HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules
  2. Khatkar, Pooja; Mensah, Gifty; Ning, Shangbo; Cowen, Maria; Kim, Yuriy; Williams, Anastasia; Abulwerdi, Fardokht A; Zhao, Yunjie; Zeng, Chen; Le Grice, Stuart F J; Kashanchi, Fatah
  3. Pharmaceuticals (Basel, Switzerland). 2023, Dec 25; 17(1):
  1. 6.   Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation
  2. Stahlberg,Eric; Abdel-Rahman, Mohamed; Aguilar, Boris; Asadpoure, Alireza; Beckman, Robert A; Borkon,Lynn; Bryan, Jeffrey N; Cebulla, Colleen M; Chang, Young Hwan; Chatterjee, Ansu; Deng, Jun; Dolatshahi, Sepideh; Gevaert, Olivier; Greenspan, Emily J; Hao, Wenrui; Hernandez-Boussard, Tina; Jackson, Pamela R; Kuijjer, Marieke; Lee, Adrian; Macklin, Paul; Madhavan, Subha; McCoy, Matthew D; Mohammad Mirzaei, Navid; Razzaghi, Talayeh; Rocha, Heber L; Shahriyari, Leili; Shmulevich, Ilya; Stover, Daniel G; Sun, Yi; Syeda-Mahmood, Tanveer; Wang, Jinhua; Wang, Qi; Zervantonakis, Ioannis
  3. Frontiers in Digital Health. 2022, Oct 6; 4: 1007784.
  1. 7.   Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
  2. Ingólfsson, Helgi I; Neale, Chris; Carpenter, Timothy S; Shrestha,Rebika; López, Cesar A; Tran, Timothy H; Oppelstrup, Tomas; Bhatia, Harsh; Stanton, Liam G; Zhang, Xiaohua; Sundram, Shiv; Di Natale, Francesco; Agarwal, Animesh; Dharuman, Gautham; Kokkila Schumacher, Sara I L; Turbyville,Tommy; Gulten, Gulcin; Van, Que N; Goswami, Debanjan; Jean-Francois, Frantz; Agamasu, Constance; Chen, De; Hettige, Jeevapani J; Travers, Timothy; Sarkar, Sumantra; Surh, Michael P; Yang, Yue; Moody, Adam; Liu, Shusen; Van Essen, Brian C; Voter, Arthur F; Ramanathan, Arvind; Hengartner, Nicolas W; Simanshu, Dhirendra K; Stephen, Andrew G; Bremer, Peer-Timo; Gnanakaran, S; Glosli, James N; Lightstone, Felice C; McCormick, Frank; Nissley, Dwight V; Streitz, Frederick H
  3. Proceedings of the National Academy of Sciences of the United States of America. 2022, Jan 04; 119(1):
  1. 8.   Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family
  2. Brown, Kevin M; Xu, Mai; Sargen, Michael; Jang,Hyunbum; Zhang,Mingzhen; Zhang, Tongwu; Zhu, Bin; Jones, Kristie; Kim, Jung; Mendoza, Laura; Hayward, Nicholas K; Tucker, Margaret A; Goldstein, Alisa M; Yang, Xiaohong Rose; Stewart, Douglas R; Hicks, Belynda; Consonni, Dario; Pesatori, Angela C; Fargnoli, Maria Concetta; Peris, Ketty; Stratigos, Alex; Menin, Chiara; Ghiorzo, Paola; Puig, Susana; Nagore, Eduardo; Andresson,Thorkell; Nussinov,Ruth; Calista, Donato; Landi, Maria Teresa
  3. Familial cancer. 2021, Jul 03;
  1. 9.   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. 10.   Inter-Institutional Partnerships to Develop Veterinarian-Investigators through the NIH Comparative Biomedical Scientist Training Program Benefit One Health Goals
  2. Simpson, R. Mark; Hoover, Shelley B.; Davis, Barbara J.; Hickerson, John; Miller, Margaret A.; Kiupel, Matti; Cullen, John M.; Dwyer, Jennifer E.; Wei,Bih; Rosol, Thomas J.; Kornegay, Joe N.; Samal, Siba K.
  3. JOURNAL OF VETERINARY MEDICAL EDUCATION. 2020, OCT; 47(5): 619-631.
  1. 11.   Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway
  2. Gillies, Taryn E; Pargett, Michael; Silva, Jillian M; Teragawa, Carolyn K; McCormick, Frank; Albeck, John G
  3. Molecular systems biology. 2020, Oct; 16(10): e9518.
  1. 12.   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. 13.   Proline Metabolism in Tumor Growth and Metastatic Progression
  2. D'Aniello, Cristina; Patriarca, Eduardo J.; Phang,James; Minchiotti, Gabriella
  3. Frontiers in oncology. 2020, MAY 15; 10: 776.
  1. 14.   HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry
  2. Guven Maiorov,Emine; Hakouz, Asma; Valjevac, Sukejna; Keskin, Ozlem; Tsai,Chung-Jung; Gursoy, Attila; Nussinov,Ruth
  3. Journal of molecular biology. 2020, MAY 15; 432(11): 3395-3403.
  1. 15.   Synthesis and biological evaluation of a series of 2-(((5-akly/aryl-1H-pyrazol-3-yl)methyl)thio)-5-alkyl-6-(cyclohexylmethyl)-pyrimidin-4(3H)-ones as potential HIV-1 inhibitors
  2. Wu, Yumeng; Tang, Chengrun; Rui, Ruomei; Yang, Liumeng; Ding, Wei; Wang, Jiangyuan; Li, Yiming; Lai,Christopher; Wang, Yueping; Luo, Ronghua; Xiao, Weilie; Zhang, Hongbing; Zheng, Yongtang; He, Yanping
  3. Acta pharmaceutica Sinica. B. 2020, Mar; 10(3): 512-528.
  1. 16.   Principles Governing Establishment versus Collapse of HIV-1 Cellular Spread
  2. Hataye, Jason M; Casazza, Joseph P; Best, Katharine; Liang, C Jason; Immonen,Taina; Ambrozak, David R; Darko, Samuel; Henry, Amy R; Laboune, Farida; Maldarelli,Frank; Douek, Daniel C; Hengartner, Nicolas W; Yamamoto, Takuya; Keele,Brandon; Perelson, Alan S; Koup, Richard A
  3. Cell host & microbe. 2019, Dec 11; 26(6): 748-763.e20.
  1. 17.   Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry
  2. Guven Maiorov,Emine; Tsai,Chung-Jung; Nussinov,Ruth
  3. Frontiers in oncology. 2019, Nov 15; 9: 1236.
  1. 18.   AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing
  2. Bhattacharya, Tanmoy; Brettin, Thomas; Doroshow, James H.; Evrard,Yvonne; Greenspan, Emily J.; Gryshuk, Amy L.; Hoang, Thuc T.; Lauzon, Carolyn B. Vea; Nissley,Dwight; Penberthy, Lynne; Stahlberg,Eric; Stevens, Rick; Streitz, Fred; Tourassi, Georgia; Xia, Fangfang; Zaki,George
  3. Frontiers in oncology. 2019, Oct 2; 9
  1. 19.   Adaptive viral load monitoring frequency to facilitate differentiated care: a modeling study from Rakai, Uganda
  2. Ssempijja,Victor; Nason, Martha; Nakigozi, Gertrude; Ndyanabo, Anthony; Gray, Ron; Wawer, Maria; Chang, Larry W; Gabriel, Erin; Quinn, Thomas C; Serwadda, David; Reynolds, Steven J
  3. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2019, Sep 18; 71(4): 1017-1021.
  1. 20.   Integrating data and knowledge to identify functional modules of genes: a multilayer approach
  2. Liang, Lifan; Chen,Vicky; Zhu, Kunju; Fan, Xiaonan; Lu, Xinghua; Lu, Songjian
  3. BMC bioinformatics. 2019, May 02; 20(1): 225.
  1. 21.   Meeting report: Fourth Summer School on Innovative Approaches for Identification of Antiviral Agents (IAAASS)
  2. Le Grice,Stuart; Maccioni, Elias; Corona, Angela; Parolin, Cristina; Tramontano, Enzo
  3. Antiviral research. 2019, Feb; 162: 110-117.
  1. 22.   Computational Structural Biology: Successes, Future Directions, and Challenges
  2. Nussinov, Ruth; Tsai, Chung-Jung; Shehu, Amarda; Jang, Hyunbum
  3. Molecules (Basel, Switzerland). 2019, Feb 1; 24(3):
  1. 23.   CYR61/CCN1 Regulates Sclerostin Levels and Bone Maintenance
  2. Zhao, Gexin; Huang, Bau-Lin; Rigueur, Diana; Wang, Weiguang; Bhoot, Chimay; Charles, Kemberly R; Baek, Jongseung; Mohan, Subburaman; Jiang, Jie; Lyons, Karen M
  3. Journal of Bone and Mineral Research. 2018, Jun; 33(6): 1076-1089.
  1. 24.   Efficacies of Cabotegravir and Bictegravir against drug-resistant HIV-1 integrase mutants
  2. Smith, Steven; Zhao, Xue Zhi; Burke, Terrence; Hughes, Stephen
  3. Retrovirology. 2018, May 16; 15(1): 37.
  1. 25.   The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
  2. Ricketts, Christopher J; De Cubas, Aguirre A; Fan, Huihui; Smith, Christof C; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A; Akbani, Rehan; Beroukhim, Rameen; Bottaro, Donald P; Choueiri, Toni K; Gibbs, Richard A; Godwin, Andrew K; Haake, Scott; Hakimi, A Ari; Henske, Elizabeth P; Hsieh, James J; Ho, Thai H; Kanchi, Rupa S; Krishnan, Bhavani; Kwaitkowski, David J; Lui, Wembin; Merino, Maria J; Mills, Gordon B; Myers, Jerome; Nickerson, Michael L; Reuter, Victor E; Schmidt, Laura S; Shelley, C Simon; Shen, Hui; Shuch, Brian; Signoretti, Sabina; Srinivasan, Ramaprasad; Tamboli, Pheroze; Thomas, George; Vincent, Benjamin G; Vocke, Cathy D; Wheeler, David A; Yang, Lixing; Kim, William T; Robertson, A Gordon; Spellman, Paul T; Rathmell, W Kimryn; Linehan, W Marston
  3. Cell Reports. 2018, Apr 03; 23(1): 313-326.e5.
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