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  1. 1.   A practical guide to large-scale docking
  2. Bender, Brian J.; Gahbauer, Stefan; Luttens, Andreas; Lyu, Jiankun; Webb, Chase M.; Stein, Reed M.; Fink, Elissa A.; Balius,Trent; Carlsson, Jens; Irwin, John J.; Shoichet, Brian K.
  3. Nature protocols. 2021, Oct; 16(10): 4799-4832.
  1. 2.   Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences
  2. Schneider,Tom; Jejjala, Vishnu
  3. PloS one. 2019, OCT 31; 14(10): e0222419.
  1. 3.   Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome
  2. Calkins, Erin R.; Zakrevsky,Paul; Keleshian, Vasken L.; Aguilar, Eduardo G.; Geary, Cody; Jaeger, Luc
  3. NUCLEIC ACIDS RESEARCH. 2019, Jan 10; 47(1): 480-494.
  1. 4.   Blind prediction of noncanonical RNA structure at atomic accuracy
  2. Watkins, Andrew M.; Geniesse, Caleb; Kladwang, Wipapat; Zakrevsky, Paul; Jaeger, Luc; Das, Rhiju
  3. Science Advances. 2018, May 25; 4(5): eaar5316.
  1. 5.   Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer's beta-Amyloid Peptide: Relevance to the Ion Channel Mechanism of AD Pathology
  2. Connelly, L.; Jang, H.; Arce, F. T.; Capone, R.; Kotler, S. A.; Ramachandran, S.; Kagan, B. L.; Nussinov, R.; Lal, R.
  3. Journal of Physical Chemistry B. 2012, Feb; 116(5): 1728-1735.
  1. 6.   Cyclostreptin Derivatives Specifically Target Cellular Tubulin and Further Map the Paclitaxel Site
  2. Calvo, E.; Barasoain, I.; Matesanz, R.; Pera, B.; Camafeita, E.; Pineda, O.; Hamel, E.; Vanderwal, C. D.; Andreu, J. M.; Lopez, J. A.; Diaz, J. F.
  3. Biochemistry. 2012, Jan; 51(1): 329-341.
  1. 7.   Small molecule inhibitors of ezrin inhibit the invasive phenotype of osteosarcoma cells
  2. Bulut, G.; Hong, S. H.; Chen, K.; Beauchamp, E. M.; Rahim, S.; Kosturko, G. W.; Glasgow, E.; Dakshanamurthy, S.; Lee, H. S.; Daar, I.; Toretsky, J. A.; Khanna, C.; Uren, A.
  3. Oncogene. 2012, Jan; 31(3): 269-281.
  1. 8.   Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
  2. Tuncbag, N.; Gursoy, A.; Nussinov, R.; Keskin, O.
  3. Nature Protocols. 2011, Sep; 6(9): 1341-1354.
  1. 9.   HIV-1 adaptation to NK-cell-mediated immune pressure
  2. Alter, G.; Heckerman, D.; Schneidewind, A.; Fadda, L.; Kadie, C. M.; Carlson, J. M.; Oniangue-Ndza, C.; Martin, M.; Li, B.; Khakoo, S. I.; Carrington, M.; Allen, T. M.; Altfeld, M.
  3. Nature. 2011, Aug; 476(7358): 96-+.
  1. 10.   HIV-1 Nucleocapsid Protein Increases Strand Transfer Recombination by Promoting Dimeric G-quartet Formation
  2. Shen, W.; Gorelick, R. J.; Bambara, R. A.
  3. Journal of Biological Chemistry. 2011, Aug; 286(34): 29838-29847.
  1. 11.   Diverse interactions of retroviral Gag proteins with RNAs
  2. Rein, A.; Datta, S. A. K.; Jones, C. P.; Musier-Forsyth, K.
  3. Trends in Biochemical Sciences. 2011, Jul; 36(7): 373-380.
  1. 12.   Interactions of Halichondrin B and Eribulin with Tubulin
  2. Bai, R. L.; Nguyen, T. L.; Burnett, J. C.; Atasoylu, O.; Munro, M. H. G.; Pettit, G. R.; Smith, A. B.; Gussio, R.; Hamel, E.
  3. Journal of Chemical Information and Modeling. 2011, Jun; 51(6): 1393-1404.
  1. 13.   Monoclonal Antibody m18 Paratope Leading to Dual Receptor Antagonism of HIV-1 gp120
  2. Gift, S. K.; McFadden, K.; Zentner, I. J.; Rajagopal, S.; Zhang, M. Y.; Dimitrov, D. S.; Chaiken, I. M.
  3. Biochemistry. 2011, Apr; 50(14): 2769-2779.
  1. 14.   Conformational and Structural Features of HIV-1 gp120 Underlying the Dual Receptor Antagonism by Cross-Reactive Neutralizing Antibody m18
  2. Gift, S. K.; Zentner, I. J.; Schon, A.; McFadden, K.; Umashankara, M.; Rajagopal, S.; Contarino, M.; Duffy, C.; Courter, J. R.; Zhang, M. Y.; Gershoni, J. M.; Cocklin, S.; Dimitrov, D. S.; Smith, A. B.; Freire, E.; Chaiken, I. M.
  3. Biochemistry. 2011, Apr; 50(14): 2756-2768.
  1. 15.   Bifunctional fusion proteins of the human engineered antibody domain m36 with human soluble CD4 are potent inhibitors of diverse HIV-1 isolates
  2. Chen, W. Z.; Xiao, X. D.; Wang, Y. P.; Zhu, Z. Y.; Dimitrov, D. S.
  3. Antiviral Research. 2010, Oct; 88(1): 107-115.
  1. 16.   Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery
  2. Ozbabacan, S. E. A.; Gursoy, A.; Keskin, O.; Nussinov, R.
  3. Current Opinion in Drug Discovery & Development. 2010, Sep; 13(5): 527-537.
  1. 17.   How Does the Reductase Help To Regulate the Catalytic Cycle of Cytochrome P450 3A4 Using the Conserved Water Channel?
  2. Fishelovitch, D.; Shaik, S.; Wolfson, H. J.; Nussinov, R.
  3. Journal of Physical Chemistry B. 2010, May; 114(17): 5964-5970.
  1. 18.   HIV-1 Transmission by Dendritic Cell-specific ICAM-3-grabbing Nonintegrin (DC-SIGN) Is Regulated by Determinants in the Carbohydrate Recognition Domain That Are Absent in Liver/Lymph Node-SIGN (L-SIGN)
  2. Chung, N. P. Y.; Breun, S. K. J.; Bashirova, A.; Baumann, J. G.; Martin, T. D.; Karamchandani, J. M.; Rausch, J. W.; Le Grice, S. F. J.; Wu, L.; Carrington, M.; KewalRamani, V. N.
  3. Journal of Biological Chemistry. 2010, Jan 15; 285(3): 2100-2112.
  1. 19.   Potent and broad neutralizing activity of a single chain antibody fragment against cell-free and cell-associated HIV-1
  2. Zhang, M. Y.; Borges, A. R.; Ptak, R. G.; Wang, Y. P.; Dimitrov, A. S.; Alam, S. M.; Wieczorek, L.; Bouma, P.; Fouts, T.; Jiang, S. B.; Polonis, V. R.; Haynes, B. F.; Quinnan, G. V.; Montefiori, D. C.; Dimitrov, D. S.
  3. Mabs. 2010, May-Jun; 2(3): 266-274.
  1. 20.   C-terminal Domain Modulates the Nucleic Acid Chaperone Activity of Human T-cell Leukemia Virus Type 1 Nucleocapsid Protein via an Electrostatic Mechanism
  2. Qualley, D. F.; Stewart-Maynard, K. M.; Wang, F.; Mitra, M.; Gorelick, R. J.; Rouzina, I.; Williams, M. C.; Musier-Forsyth, K.
  3. Journal of Biological Chemistry. 2010, Jan; 285(1): 295-307.
  1. 21.   Features, processing states and heterologous protein interactions in the modulation of the retroviral nucleocapsid protein function
  2. Mirambeau, G.; Lyonnais, S.; Gorelick, R. J.
  3. Rna Biology. 2010, Nov-Dec; 7(6): 724-734.
  1. 22.   Nucleic acid chaperone activity of retroviral Gag proteins
  2. Rein, A.
  3. Rna Biology. 2010, Nov-Dec; 7(6): 700-705.
  1. 23.   Maturation Pathways of Cross-Reactive HIV-1 Neutralizing Antibodies
  2. Xiao, X. D.; Chen, W. Z.; Feng, Y.; Dimitrov, D. S.
  3. Viruses-Basel. 2009, Dec; 1(3): 802-817.
  1. 24.   Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120
  2. Chen, L.; Kwon, Y. D.; Zhou, T. Q.; Wu, X. L.; O'Dell, S.; Cavacini, L.; Hessell, A. J.; Pancera, M.; Tang, M.; Xu, L.; Yang, Z. Y.; Zhang, M. Y.; Arthos, J.; Burton, D. R.; Dimitrov, D. S.; Nabel, G. J.; Posner, M. R.; Sodroski, J.; Wyatt, R.
  3. Science. 2009 326(5956): 1123-1127.
  1. 25.   Association Energetics of Cross-Reactive and Specific Antibodies
  2. Mohan, S.; Kourentzi, K.; Schick, K. A.; Uehara, C.; Lipschultz, C. A.; Acchione, M.; DeSantis, M. E.; Smith-Gill, S. J.; Willson, R. C.
  3. Biochemistry. 2009 48(6): 1390-1398.
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