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  1. 1.   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. 2.   Integration of Computational Docking into Anti-Cancer Drug Response Prediction Models
  2. Narykov, Oleksandr; Zhu, Yitan; Brettin, Thomas; Evrard,Yvonne; Partin, Alexander; Shukla, Maulik; Xia, Fangfang; Clyde, Austin; Vasanthakumari, Priyanka; Doroshow, James H; Stevens, Rick L
  3. Cancers. 2023, Dec 21; 16(1):
  1. 3.   Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions
  2. Guo, Sikao; Saha,Ipsita; Saffarian, Saveez; Johnson, Margaret E
  3. eLife. 2023, Jul 12; 12
  1. 4.   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. 5.   BETA: a comprehensive benchmark for computational drug-target prediction
  2. Zong, Nansu; Li,Ning; Wen, Andrew; Ngo, Victoria; Yu, Yue; Huang, Ming; Chowdhury, Shaika; Jiang, Chao; Fu, Sunyang; Weinshilboum, Richard; Jiang, Guoqian; Hunter, Lawrence; Liu, Hongfang
  3. Briefings in Bioinformatics. 2022, Jun 02;
  1. 6.   Coumarin luciferins and mutant luciferases for robust multi-component bioluminescence imaging
  2. Yao, Zi; Caldwell,Donald; Love, Anna C.; Kolbaba-Kartchner, Bethany; Mills, Jeremy H.; Schnermann,Martin; Prescher, Jennifer A.
  3. CHEMICAL SCIENCE. 2021, Aug 2;
  1. 7.   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. 8.   Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens
  2. Ueda, George; Antanasijevic, Aleksandar; Fallas, Jorge A; Sheffler, William; Copps, Jeffrey; Ellis, Daniel; Hutchinson, Geoffrey B; Moyer, Adam; Yasmeen, Anila; Tsybovsky,Yaroslav; Park, Young-Jun; Bick, Matthew J; Sankaran, Banumathi; Gillespie, Rebecca A; Brouwer, Philip Jm; Zwart, Peter H; Veesler, David; Kanekiyo, Masaru; Graham, Barney S; Sanders, Rogier W; Moore, John P; Klasse, Per Johan; Ward, Andrew B; King, Neil P; Baker, David
  3. eLife. 2020, Aug 04; 9: pii: 9:e57659.
  1. 9.   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. 10.   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. 11.   Evidence for ligandable sites in structured RNA throughout the Protein Data Bank
  2. Hewitt, William M.; Calabrese,Dave; Schneekloth,Jay
  3. BIOORGANIC & MEDICINAL CHEMISTRY. 2019, Jun 1; 27(11): 2253-2260.
  1. 12.   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. 13.   Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer
  2. Guven-Maiorov, Emine; Tsai, Chung-Jung; Ma, Buyong; Nussinov, Ruth
  3. Journal of molecular biology. 2017, Dec 8; 429(24): 3925-3941.
  1. 14.   A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids.
  2. Haspel, Nurit; Zheng, Jie; Aleman, Carlos; Zanuy, David; Nussinov, Ruth
  3. Methods in molecular biology (Clifton, N.J.). 2017 1529: 323-352.
  1. 15.   Integrating Epigenomics into the Understanding of Biomedical Insight.
  2. Han, Yixing; He, Ximiao
  3. Bioinformatics and biology insights. 2016, Dec 4; 10: 267-289.
  1. 16.   MPGAfold in dengue secondary structure prediction
  2. Kasprzak, W. K.; Shapiro, B. A.
  3. Methods in molecular biology (Clifton, N.J.). 2014, 20-Feb; 1138: 199-224.
  1. 17.   CCRXP: exploring clusters of conserved residues in protein structures
  2. Ahmad, S.; Keskin, O.; Mizuguchi, K.; Sarai, A.; Nussinov, R.
  3. Nucleic Acids Research. 2010, Jul; 38: W398-W401.
  1. 18.   Comparison of Nine Programs Predicting pK(a) Values of Pharmaceutical Substances
  2. Liao, C. Z.; Nicklaus, M. C.
  3. Journal of Chemical Information and Modeling. 2009, Dec; 49(12): 2801-2812.
  1. 19.   Rotational order-disorder structure of fluorescent protein FP480
  2. Pletnev, S.; Morozova, K. S.; Verkhusha, V. V.; Dauter, Z.
  3. Acta crystallographica. Section D, Biological crystallography. 2009, Sep; 65(Pt 9): 906-12.
  1. 20.   Structural similarity of genetically interacting proteins
  2. Dror, O.; Schneidman-Duhovny, D.; Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J.; Sharan, R.
  3. BMC Systems Biology. 2008 2 AR 69
  1. 21.   Polymorphism Interaction Analysis (PIA): A method for investigating complex gene-gene interactions
  2. Mechanic, L. E.; Luke, B. T.; Goodman, J. E.; Chanock, S. J.; Harris, C. C.
  3. Bmc Bioinformatics. 2008 9 AR 146 DI 10.1186/
  1. 22.   Protocols for the in silico design of RNA nanostructures
  2. Shapiro, B. A.; Bindewald, E.; Kasprzak, W.; Yingling, Y.
  3. Methods in molecular biology (Clifton, N.J.). 2008 474: 93-115.
  1. 23.   Internet resources integrating many small-molecule databases
  2. Sitzmann, M.; Filippov, I. V.; Nicklaus, M. C.
  3. SAR and QSAR in Environmental Research. 2008 19(1-2): 1-9.
  1. 24.   Computational prediction of proteotypic peptides
  2. Blonder, J.; Veenstra, T. D.
  3. Expert Review of Proteomics. 2007, Jun; 4(3): 351-354.
  1. 25.   Towards drugs targeting multiple proteins in a systems biology approach
  2. Keskin, O.; Gursoy, A.; Ma, B.; Nussinov, R.
  3. Current Topics in Medicinal Chemistry. 2007 7(10): 943-951.
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