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  1. 1.   MoCoLo: a testing framework for motif co-localization
  2. Xu, Qi; Del Mundo, Imee M A; Zewail-Foote, Maha; Luke,Brian; Vasquez, Karen M; Kowalski, Jeanne
  3. Briefings in Bioinformatics. 2024, Jan 22; 25(2):
  1. 2.   Human gammaS-Crystallin Mutation F10_Y11delinsLN in the First Greek Key Pair Destabilizes and Impairs Tight Packing Causing Cortical Lamellar Cataract
  2. Vendra, Venkata Pulla Rao; Ostrowski, Christian; Dyba, Marzena A; Tarasov,Sergey; Hejtmancik, J Fielding
  3. International Journal of Molecular Sciences. 2023, Sep 20; 24(18):
  1. 3.   Crystal Structure of an i-Motif from the HRAS Oncogene Promoter
  2. Li, Kevin S; Jordan, Deondre; Lin, Linda Y; McCarthy, Sawyer E; Schneekloth,Jay; Yatsunyk, Liliya A
  3. Angewandte Chemie (International ed. in English). 2023, Mar 30; e202301666.
  1. 4.   The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores
  2. Shen, Qi; Kumari, Sushila; Xu, Chaoyi; Jang, Sooin; Shi, Jiong; Burdick,Ryan; Levintov, Lev; Xiong, Qiancheng; Wu, Chunxiang; Devarkar, Swapnil C; Tian, Taoran; Tripler, Therese N; Hu, Yingxia; Yuan, Shuai; Temple, Joshua; Feng, Qingzhou; Lusk, C Patrick; Aiken, Christopher; Engelman, Alan N; Perilla, Juan R; Pathak,Vinay; Lin, Chenxiang; Xiong, Yong
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Mar 28; 120(13): e2202815120.
  1. 5.   Structural basis for cell type specific DNA binding of C/EBPß: the case of cell cycle inhibitor p15INK4b promoter
  2. Lountos, George T; Cherry, Scott; Tropea, Joseph E; Wlodawer, Alexander; Miller, Maria
  3. Journal of Structural Biology. 2022, Nov 04; 214(4): 107918.
  1. 6.   dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data
  2. Ou, Jianhong; Liu, Haibo; Nirala, Niraj K.; Stukalov, Alexey; Acharya,Usha; Green, Michael R.; Zhu, Lihua Julie
  3. PLOS ONE. 2020, NOV 6; 15(11):
  1. 7.   SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations
  2. Liao, Tsung-Jen; Jang,Hyunbum; Fushman, David; Nussinov,Ruth
  3. The Journal of chemical physics. 2020, Jul 28; 153(4): 045106.
  1. 8.   High-Affinity Interactions of the nSH3/cSH3 Domains of Grb2 with the C-Terminal Proline-Rich Domain of SOS1
  2. Liao,Tsung-Jen; Jang,Hyunbum; Nussinov,Ruth; Fushman, David
  3. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2020, Feb 19; 142: 3401-3411.
  1. 9.   An ultra-stable redox-controlled self-assembling polypeptide nanotube for targeted imaging and therapy in cancer
  2. Asampille, Gitanjali; Verma, Brijesh Kumar; Swain, Monalisa; Shettar, Abhijith; Rosenzweig, Steven A; Kondaiah, Paturu; Atreya, Hanudatta S
  3. Journal of nanobiotechnology. 2018, Dec 08; 16(1): 101.
  1. 10.   Calmodulin and IQGAP1 activation of PI3K alpha and Akt in KRAS, HRAS and NRAS-driven cancers
  2. Nussinov, Ruth; Zhang, Mingzhen; Tsai, Chung-Jung; Jang, Hyunbum
  3. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE. 2018, Jun; 0925-4439:(6, Part B, Special Issue): 2304-2314.
  1. 11.   Cooperative Domain Formation by Homologous Motifs in HOIL-1L and SHARPIN Plays A Crucial Role in LUBAC Stabilization
  2. Fujita, Hiroaki; Tokunaga, Akira; Shimizu, Satoshi; Whiting, Amanda L; Aguilar Alonso, Francisco; Takagi, Kenji; Walinda, Erik; Sasaki, Yoshiteru; Shimokawa, Taketo; Mizushima, Tsunehiro; Ohki, Izuru; Ariyoshi, Mariko; Tochio, Hidehito; Bernal, Federico; Shirakawa, Masahiro; Iwai, Kazuhiro
  3. Cell Reports. 2018, Apr 24; 23(4): 1192-1204.
  1. 12.   Effect of Calcium Carbonate Encapsulation on the Activity of Orally Administered CpG Oligonucleotides
  2. Kayraklioglu, Neslihan; Scheiermann, Julia; Alvord, W. Gregory; Klinman, Dennis
  3. MOLECULAR THERAPY-NUCLEIC ACIDS. 2017, Sep 15; 8: 243-249.
  1. 13.   Dynamic conformational changes in the rhesus TRIM5alpha dimer dictate the potency of HIV-1 restriction
  2. Lamichhane, R.; Mukherjee, S.; Smolin, N.; Pauszek, R. F., 3rd; Bradley, M.; Sastri, J.; Robia, S. L.; Millar, D.; Campbell, E. M.
  3. Virology. 2016, Jan; 500: 161-168.
  1. 14.   MDM1 is a microtubule-binding protein that negatively regulates centriole duplication
  2. Van de Mark, D.; Kong, D.; Loncarek, J.; Stearns, T.
  3. Molecular Biology of the Cell. 2015, 1-Nov; 26(21): 3788-802.
  1. 15.   Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement
  2. Tuncbag, N.; Keskin, O.; Nussinov, R.; Gursoy, A.
  3. Proteins-Structure Function and Bioinformatics. 2012, Apr; 80(4): 1239-1249.
  1. 16.   Antimicrobial Properties of Amyloid Peptides
  2. Kagan, B. L.; Jang, H.; Capone, R.; Arce, F. T.; Ramachandran, S.; Lal, R.; Nussinov, R.
  3. Molecular Pharmaceutics. 2012, Apr; 9(4): 708-717.
  1. 17.   RanBPM is essential for mouse spermatogenesis and oogenesis
  2. Puverel, S.; Barrick, C.; Dolci, S.; Coppola, V.; Tessarollo, L.
  3. Development. 2011, Jun; 138(12): 2511-2521.
  1. 18.   The acceleration of wound healing in primates by the local administration of immunostimulatory CpG oligonucleotides
  2. Yamamoto, M.; Sato, T.; Beren, J.; Verthelyi, D.; Klinman, D. M.
  3. Biomaterials. 2011, Jun; 32(18): 4238-4242.
  1. 19.   Self-Assembling RNA Nanorings Based on RNAI/II Inverse Kissing Complexes
  2. Grabow, W. W.; Zakrevsky, P.; Afonin, K. A.; Chworos, A.; Shapiro, B. A.; Jaeger, L.
  3. Nano Letters. 2011, Feb; 11(2): 878-887.
  1. 20.   Measuring cooperative Rev protein-protein interactions on Rev responsive RNA by fluorescence resonance energy transfer
  2. Vercruysse, T.; Pawar, S.; De Borggraeve, W.; Pardon, E.; Pavlakis, G. N.; Pannecouque, C.; Steyaert, J.; Balzarini, J.; Daelemans, D.
  3. Rna Biology. 2011, Mar-Apr; 8(2): 316-324.
  1. 21.   beta-Barrel Topology of Alzheimer's beta-Amyloid Ion Channels
  2. Jang, H.; Arce, F. T.; Ramachandran, S.; Capone, R.; Lal, R.; Nussinov, R.
  3. Journal of Molecular Biology. 2010, Dec; 404(5): 917-934.
  1. 22.   Crystallographic and Functional Analysis of the ESCRT-I/HIV-1 Gag PTAP Interaction
  2. Im, Y. J.; Kuo, L.; Ren, X. F.; Burgos, P. V.; Zhao, X. Z.; Liu, F.; Burke, T. R.; Bonifacino, J. S.; Freed, E. O.; Hurley, J. H.
  3. Structure. 2010, Nov; 18(11): 1536-1547.
  1. 23.   Why Does Binding of Proteins to DNA or Proteins to Proteins Not Necessarily Spell Function?
  2. Ma, B. Y.; Tsai, C. J.; Pan, Y. P.; Nussinov, R.
  3. Acs Chemical Biology. 2010, Mar; 5(3): 265-272.
  1. 24.   Short- and long-term changes in gene expression mediated by the activation of TLR9
  2. Klaschik, S.; Tross, D.; Shirota, H.; Klinman, D. M.
  3. Molecular Immunology. 2010, Mar; 47(6): 1317-1324.
  1. 25.   Immunostimulatory CpG oligonucleotides: Effect on gene expression and utility as vaccine adjuvants
  2. Klinman, D. M.; Klaschik, S.; Tomaru, K.; Shirota, H.; Tross, D.; Ikeuchi, H.
  3. Vaccine. 2010, Feb; 28(8): 1919-1923.
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