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  1. 1.   Cross-linking mass spectrometry for mapping protein complex topologies in situ
  2. Lee,Kitaik; O'Reilly,Francis
  3. Essays in Biochemistry. 2023, Feb 03;
  1. 2.   The tumor suppressor activity of DLC1 requires the interaction of its START domain with Phosphatidylserine, PLCD1, and Caveolin-1
  2. Sanchez-Solana, Beatriz; Wang, Dunrui; Qian, Xiaolan; Velayoudame, Parthibane; Simanshu,Dhirendra; Acharya,Jairaj; Lowy, Douglas R
  3. Molecular Cancer. 2021, Nov 02; 20(1):
  1. 3.   Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI
  2. Li,Mi; Srp, Jaroslav; Mares, Michael; Wlodawer,Alexander; Gustchina,Alla
  3. Acta crystallographica. Section D, Structural biology. 2021, Aug 1; 77(Pt 8): 1084-1098.
  1. 4.   The viral protein U (Vpu)-interacting host protein ATP6V0C down-regulates cell-surface expression of tetherin and thereby contributes to HIV-1 release
  2. Waheed,Abdul; Swiderski, Maya; Khan, Ali; Gitzen, Ariana; Majadly, Ahlam; Freed,Eric
  3. The Journal of Biological Chemistry. 2020, MAY 22; 295(21): 7327-7340.
  1. 5.   Developments in integrative modeling with dynamical interfaces
  2. Ozdemir, E. Sila; Nussinov,Ruth; Gursoy, Attila; Keskin, Ozlem
  3. CURRENT OPINION IN STRUCTURAL BIOLOGY. 2019, Jun; 56: 11-17.
  1. 6.   Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers
  2. Nussinov,Ruth; Jang,Hyunbum; Tsai,Chung-Jung; Cheng, Feixiong
  3. PLoS computational biology. 2019, Mar; 15(3):
  1. 7.   Biophysical and biological evaluation of optimized stapled peptide inhibitors of the linear ubiquitin chain assembly complex (LUBAC)
  2. Aguilar Alonso, Francisco; Whiting, Amanda L.; Kim, Ye Joon; Bernal, Federico
  3. BIOORGANIC & MEDICINAL CHEMISTRY. 2018, Mar 15; 26(6): 1179-1188.
  1. 8.   Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex
  2. Guo, Tai Wei; Bartesaghi, Alberto; Yang, Hui; Falconieri, Veronica; Rao, Prashant; Merk, Alan; Eng, Edward T; Raczkowski, Ashleigh M; Fox, Tara; Earl, Lesley A; Patel, Dinshaw J; Subramaniam, Sriram
  3. Cell. 2017, Oct 05; 171(2): 414-426.e12.
  1. 9.   A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution
  2. Shelley, Mee Y.; SeIvan, Myvizhi Esai; Zhao, Jun; Babin, Volodymyr; Liao, Chenyi; Li, Jianing; Shelley, John C.
  3. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2017, Aug; 13(8): 3881-3897.
  1. 10.   The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2
  2. Jha, Jyoti K; Li, Mi; Ghirlando, Rodolfo; Miller Jenkins, Lisa M; Wlodawer, Alexander; Chattoraj, Dhruba
  3. mBio. 2017, Apr 18; 8(2):
  1. 11.   Crystal Structure of a Complex of the Intracellular Domain of Interferon lambda Receptor 1 (IFNLR1) and the FERM/SH2 Domains of Human JAK1
  2. Zhang, D.; Wlodawer, A.; Lubkowski, J.
  3. Journal of Molecular Biology. 2016, 2016-11-20; 428(23): 4651-4668.
  1. 12.   How do dynamic cellular signals travel long distances?
  2. Nussinov, R.
  3. Molecular Biosystems. 2012, Jan 1; 8(1): 22-26.
  1. 13.   Elucidation of New Binding Interactions with the Human Tsg101 Protein Using Modified HIV-1 Gag-p6 Derived Peptide Ligands
  2. Kim, S. E.; Liu, F.; Im, Y. J.; Stephen, A. G.; Fivash, M. J.; Waheed, A. A.; Freed, E. O.; Fisher, R. J.; Hurley, J. H.; Burke, T. R.
  3. Acs Medicinal Chemistry Letters. 2011, May; 2(5): 337-341.
  1. 14.   Peptide Structure Stabilization by Membrane Anchoring and its General Applicability to the Development of Potent Cell-Permeable Inhibitors
  2. Johannessen, L.; Remsberg, J.; Gaponenko, V.; Adams, K. M.; Barchi, J. J.; Tarasov, S. G.; Jiang, S.; Tarasova, N. I.
  3. Chembiochem. 2011, Apr; 12(6): 914-921.
  1. 15.   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. 16.   Limitations of Peptide Retro-inverso Isomerization in Molecular Mimicry
  2. Li, C.; Pazgier, M.; Li, J.; Li, C. Q.; Liu, M.; Zou, G. Z.; Li, Z. Y.; Chen, J. D.; Tarasov, S. G.; Lu, W. Y.
  3. Journal of Biological Chemistry. 2010, Jun; 285(25): 19572-19581.
  1. 17.   Fiber Dock: Flexible induced-fit backbone refinement in molecular docking
  2. Mashiach, E.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2010, May; 78(6): 1503-1519.
  1. 18.   12 Arylstibonic acids that inhibit the DNA binding of five B-ZIP dimers
  2. Rishi, V.; Oh, W. J.; Heyerdahl, S. L.; Zhao, J. F.; Scudiero, D.; Shoemaker, R. H.; Vinson, C.
  3. Journal of Structural Biology. 2010, May; 170(2): 216-225.
  1. 19.   Energetic determinants of protein binding specificity: Insights into protein interaction networks
  2. Carbonell, P.; Nussinov, R.; del Sol, A.
  3. Proteomics. 2009 9(7): 1744-1753.
  1. 20.   Preparation of orthogonally protected (2S,3R)-2-amino-3-methyl-4-phosphonobutyric acid (Pmab) as a phosphatase-stable phosphothreonine mimetic and its use in the synthesis of polo-box domain-binding peptides
  2. Liu, F.; Park, J. E.; Lee, K. S.; Burke, T. R.
  3. Tetrahedron. 2009 65(47): 9673-9679.
  1. 21.   Transposition into Replicating DNA Occurs through Interaction with the Processivity Factor
  2. Parks, A. R.; Li, Z. P.; Shi, Q. J.; Owens, R. M.; Jin, M. M.; Peters, J. E.
  3. Cell. 2009 138(4): 685-695.
  1. 22.   Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX
  2. Pazgiera, M.; Liu, M.; Zou, G. Z.; Yuan, W. R.; Li, C. Q.; Li, C.; Li, J.; Monbo, J.; Zella, D.; Tarasov, S. G.; Lu, W.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2009 106(12): 4665-4670.
  1. 23.   Structural Basis of Focal Adhesion Localization of LIM-only Adaptor PINCH by Integrin-linked Kinase
  2. Yang, Y. W.; Wang, X. X.; Hawkins, C. A.; Chen, K.; Vaynberg, J.; Mao, X.; Tu, Y. Z.; Zuo, X. B.; Wang, J. B.; Wang, Y. X.; Wu, C. Y.; Tjandra, N.; Qin, J.
  3. Journal of Biological Chemistry. 2009 284(9): 5836-5844.
  1. 24.   SAR by oxime-containing peptide libraries: Application to Tsg101 ligand optimization
  2. Liu, F.; Stephen, A. G.; Waheed, A. A.; Aman, M. J.; Freed, E. O.; Fisher, R. J.; Burke, T. R.
  3. Chembiochem. 2008 9(12): 2000-2004.
  1. 25.   An enzymatically activated fluorescence probe for targeted tumor imaging
  2. Kamiya, M.; Kobayashi, H.; Hama, Y.; Koyama, Y.; Bernardo, M.; Nagano, T.; Choyke, P. L.; Urano, Y.
  3. Journal of the American Chemical Society. 2007, Apr; 129(13): 3918-3929.
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