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  1. 1.   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. 2.   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. 3.   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. 4.   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. 5.   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.
  1. 6.   MolAxis: a server for identification of channels in macromolecules
  2. Yaffe, E.; Fishelovitch, D.; Wolfson, H. J.; Halperin, D.; Nussinov, R.
  3. Nucleic Acids Research. 2008 36(Web Server Issue): W210-W215.
  1. 7.   Interaction of noncompetitive inhibitors with the alpha 3 beta 2 nicotinic acetylcholine receptor investigated by affinity chromatography and molecular docking
  2. Jozwiak, K.; Ravichandran, S.; Collins, J. R.; Moaddel, R.; Wainer, I. W.
  3. Journal of Medicinal Chemistry. 2007, Nov; 50(24): 6279-6283.
  1. 8.   Identification of novel Wilms' tumor suppressor gene target genes implicated in kidney development
  2. Kim, H. S.; Kim, M. S.; Hancock, A. L.; Harper, J. C. P.; Park, J. Y.; Poy, G.; Perantoni, A. O.; Cam, M.; Malik, K.; Lee, S. B.
  3. Journal of Biological Chemistry. 2007, Jun; 282(22): 16278-16287.
  1. 9.   Trp/Met/Phe hot spots in protein-protein interactions: Potential targets in drug design
  2. Ma, B.; Nussinov, R.
  3. Current Topics in Medicinal Chemistry. 2007 7(10): 999-1005.
  1. 10.   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.
  1. 11.   CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
  2. Bindewald, E.; Schneider, T. D.; Shapiro, B. A.
  3. Nucleic Acids Research. 2006, Jul; 34: W405-W411.
  1. 12.   Claude Shannon: Biologist
  2. Schneider, T. D.
  3. IEEE Engineering in Medicine and Biology Magazine. 2006, JAN-FEB; 25(1): 30-33.
  1. 13.   A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach
  2. Nguyen, T. L.; McGrath, C.; Hermone, A. R.; Burnett, J. C.; Zaharevitz, D. W.; Day, B. W.; Wipf, P.; Hamel, E.; Gussio, R.
  3. Journal of Medicinal Chemistry. 2005, SEP 22; 48(19): 6107-6116.
  1. 14.   Calcium-dependent activation of interleukin-21 gene expression in T cells
  2. Kim, H. P.; Korn, L. L.; Gamero, A. M.; Leonard, W. J.
  3. Journal of Biological Chemistry. 2005, JUL 1; 280(26): 25291-25297.
  1. 15.   Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach
  2. Keskin, O.; Ma, B. Y.; Rogale, K.; Gunasekaran, K.; Nussinov, R.
  3. Physical Biology. 2005, JUN; 2(2): S24-S35.
  1. 16.   Cross-resistance of Escherichia coli RNA polymerases conferring rifarnpin resistance to different antibiotics
  2. Xu, M.; Zhou, Y. N.; Goldstein, B. P.; Jin, D. J.
  3. Journal of Bacteriology. 2005, APR; 187(8): 2783-2792.
  1. 17.   How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues
  2. Haliloglu, T.; Keskin, O.; Ma, B. Y.; Nussinov, R.
  3. Biophysical Journal. 2005, MAR; 88(3): 1552-1559.
  1. 18.   Transcriptional regulator CTCF controls human interleukin 1 receptor-associated kinase 2 promoter
  2. Kuzmin, I.; Geil, L.; Gibson, L.; Cavinato, T.; Loukinov, D.; Lobanenkov, V.; Lerman, M. I.
  3. Journal of Molecular Biology. 2005, FEB 18; 346(2): 411-422.
  1. 19.   Design and synthesis of conformationally constrained Grb2 SH2 domain binding peptides employing alpha-methylphenylalanyl based phosphotyrosyl mimetics
  2. Oishi, S.; Karki, R. G.; Kang, S. U.; Wang, X. Z.; Worthy, K. M.; Bindu, L. K.; Nicklaus, M. C.; Fisher, R. J.; Burke, T. R.
  3. Journal of Medicinal Chemistry. 2005, FEB 10; 48(3): 764-772.
  1. 20.   Recognition of binding patterns common to a set of protein structures
  2. Shatsky, M.; Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J.
  3. Research in Computational Molecular Biology, Proceedings. 2005 3500: 440-455.
  1. 21.   Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases
  2. Chen, Z. H.; Schneider, T. D.
  3. Nucleic Acids Research. 2005 33(19): 6172-6187.
  1. 22.   Interleukin-10 induces uteroglobin-related protein (UGRP) 1 gene expression in lung epithelial cells through homeodomain transcription factor T/EBP/NKX2.1
  2. Srisodsai, A.; Kurotani, R.; Chiba, Y.; Sheikh, F.; Young, H. A.; Donnelly, R. P.; Kimura, S.
  3. Journal of Biological Chemistry. 2004, DEC 24; 279(52): 54358-54368.
  1. 23.   Is allostery an intrinsic property of all dynamic proteins?
  2. Gunasekaran, K.; Ma, B. Y.; Nussinov, R.
  3. Proteins-Structure Function and Bioinformatics. 2004, NOV 15; 57(3): 433-443.
  1. 24.   Ions from the Hofmeister series and osmolytes: effects on proteins in solution and in the crystallization process
  2. Collins, K. D.
  3. Methods. 2004, NOV; 34(3): 300-311.
  1. 25.   Mammary gland remodeling depends on gp130 signaling through Stat3 and MAPK
  2. Zhao, L.; Hart, S.; Cheng, J. G.; Melenhorst, J. J.; Bierie, B.; Ernst, M.; Stewart, C.; Schaper, F.; Heinrich, P. C.; Ullrich, A.; Robinson, G. W.; Hennighausen, L.
  3. Journal of Biological Chemistry. 2004, OCT 15; 279(42): 44093-44100.
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