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  1. 1.   Machine learning-augmented molecular dynamics simulations (MD) reveal insights into the disconnect between affinity and activation of ZTP riboswitch ligands
  2. Fullenkamp, Christopher; Mehdi, Shams; Jones, Christopher; Tenney, Logan; Pichling, Patricio; Prestwood, Peri R; Ferré-D'Amaré, Adrian R; Tiwary, Pratyush; Schneekloth,John
  3. Angewandte Chemie (International ed. in English). 2025, May 01; e202505971.
  1. 2.   Optimization of the PROTAC linker region of the proteasome substrate receptor hRpn13 rationalized structural modeling with molecular dynamics
  2. Lu,Xiuxiu; Sabbasani, Venkata R; Walters,Kylie; Swenson, Rolf E; Walters,Kylie
  3. The Journal of Biological Chemistry. 2025, Apr 18; 108520.
  1. 3.   ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events
  2. Regev,Clil; Jang,Hyunbum; Nussinov,Ruth
  3. Journal of Molecular Biology. 2025, Apr 09; 169130.
  1. 4.   In some cases more complicated approaches to refinement of macromolecular structures are not necessary
  2. Dauter, Zbigniew; Wlodawer,Alexander
  3. IUCrJ. 2024, Jul 01; 11(Pt 4): 643-644.
  1. 5.   Disruption of Ca2+/calmodulin:KSR1 interaction lowers ERK activation
  2. Thines, Louise; Jang,Hyunbum; Li, Zhigang; Sayedyahossein, Samar; Maloney, Ryan; Nussinov,Ruth; Sacks, David B
  3. Protein Science : a publication of the Protein Society. 2024, May; 33(5): e4982.
  1. 6.   P1' specificity of the S219V/R203G mutant tobacco etch virus protease
  2. Golda, Mária; Hoffka, Gyula; Cherry,Scott; Tropea, Joseph E; Lountos,George; Waugh, David S; Wlodawer,Alexander; Tozsér, József; Mótyán, János András
  3. Proteins. 2024, Apr 26;
  1. 7.   Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state
  2. Lee,Hyun Kyung; Lee,Yun-Tzai; Fan,Lixin; Wilt, Haley M; Conrad, Chelsie E; Yu,Ping; Zhang, Jinwei; Shi,Genbin; Ji,Xinhua; Wang,Yun-Xing; Stagno,Jason
  3. Structure (London, England : 1993). 2023, Jul 7; 31(7): 848-859..
  1. 8.   A mutagenesis study of autoantigen optimization for potential T1D vaccine design
  2. Song, Yi; Bell,David; Ahmed, Rizwan; Chan, Kevin C; Lee, Sangyun; Hamad, Abdel Rahim A; Zhou, Ruhong
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Apr 18; 120(16): e2214430120.
  1. 9.   Virtual Screening of Hepatitis B Virus Pre-Genomic RNA as a Novel Therapeutic Target
  2. Olenginski, Lukasz T; Kasprzak, Wojciech K; Attionu, Solomon K; Shapiro, Bruce A; Dayie, Theodore K
  3. Molecules (Basel, Switzerland). 2023, Feb 14; 28(4):
  1. 10.   Self-inhibited state of Venezuelan equine encephalitis virus (VEEV) nsP2 cysteine protease: a crystallographic and molecular dynamics analysis
  2. Hoffka, Gyula; Lountos,George; Needle,Danielle; Wlodawer,Alexander; Waugh, David S; Tozsér, József; András Mótyán, János
  3. Journal of Molecular Biology. 2023, Feb 13; 435(6): 168012.
  1. 11.   The in-silico evaluation of important GLUT9 residue for uric acid transport based on renal hypouricemia type 2
  2. Cachau, Raul; Shahsavari, Shahin; Cho, Sung Kweon
  3. Chemico-Biological Interactions. 2023, Feb 01; 110378.
  1. 12.   Small GTPase Ran: Depicting the nucleotide-specific conformational landscape of the functionally important C-terminus
  2. Czigleczki, Janka; de Resende Lara, Pedro Tulio; Dudas, Balint; Jang,Hyunbum; Perahia, David; Nussinov,Ruth; Balog, Erika
  3. Frontiers in Molecular Biosciences. 2023, Jan 16; 10: 1111574.
  1. 13.   Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody
  2. Kabir, Kazi Lutful; Ma, Buyong; Nussinov,Ruth; Shehu, Amarda
  3. Biomolecules. 2022, Jul 21; 12(7): 1011.
  1. 14.   Conformational Dynamics Allows Sampling of an "Active-like" State by Oncogenic K-Ras-GDP
  2. Grudzien, Patrick; Jang,Hyunbum; Leschinsky, Nicholas; Nussinov,Ruth; Gaponenko, Vadim
  3. Journal of Molecular Biology. 2022, Jun 22; 167695.
  1. 15.   Regulation of GTPase function by autophosphorylation
  2. Johnson, Christian W; Seo, Hyuk-Soo; Terrell,Elizabeth; Yang, Moon-Hee; KleinJan, Fenneke; Gebregiworgis, Teklab; Gasmi-Seabrook, Genevieve M C; Geffken, Ezekiel A; Lakhani, Jimit; Song, Kijun; Bashyal, Puspalata; Popow, Olesja; Paulo, Joao A; Liu, Andrea; Mattos, Carla; Marshall, Christopher B; Ikura, Mitsuhiko; Morrison, Deborah K; Dhe-Paganon, Sirano; Haigis, Kevin M
  3. Molecular Cell. 2022, Feb 18; 82(5): 950-968.e14.
  1. 16.   Allosteric regulation of autoinhibition and activation of c-Abl
  2. Liu,Yonglan; Zhang,Mingzhen; Tsai,Chung-Jung; Jang,Hyunbum; Nussinov,Ruth
  3. Computational and Structural Biotechnology Journal. 2022 20: 4257-4270.
  1. 17.   The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation
  2. Lyonnais, Sébastien; Sadiq, S Kashif; Lorca-Oró, Cristina; Dufau, Laure; Nieto-Marquez, Sara; Escribà, Tuixent; Gabrielli, Natalia; Tan, Xiao; Ouizougun-Oubari, Mohamed; Okoronkwo, Josephine; Reboud-Ravaux, Michèle; Gatell, José Maria; Marquet, Roland; Paillart, Jean-Christophe; Meyerhans, Andreas; Tisné, Carine; Gorelick,Robert; Mirambeau, Gilles
  3. Viruses. 2021, Nov 19; 13(11):
  1. 18.   Evolution of Thyroglobulin Loop Kinetics in EpCAM
  2. Chen, Serena H.; Bell,David
  3. LIFE-BASEL. 2021, Sep 03; 11(9):
  1. 19.   Unveiling the Dynamics of KRAS4b on Lipid Model Membranes
  2. Lopez, Cesar A.; Agarwal, Animesh; Van,Que; Stephen,Andy; Gnanakaran, S.
  3. Journal of Membrane Biology. 2021, Apr; 254(2): 201-216.
  1. 20.   Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics
  2. Haspel, Nurit; Jang,Hyunbum; Nussinov,Ruth
  3. Biophysical journal. 2021, Jan 19; 120(2): 306-318.
  1. 21.   Nucleotide-Specific Autoinhibition of Full-Length K-Ras4B Identified by Extensive Conformational Sampling
  2. Dudas, Balint; Merzel, Franci; Jang,Hyunbum; Nussinov,Ruth; Perahia, David; Balog, Erika
  3. Frontiers in molecular biosciences. 2020, JUL 10; 7: 145.
  1. 22.   A terminal alpha 3-galactose modification regulates an E3 ubiquitin ligase subunit in Toxoplasma gondii
  2. Mandalasi, Msano; Kim, Hyun W.; Thieker, David; Sheikh, M. Osman; Gas-Pascual, Elisabet; Rahman,Kazi; Zhao, Peng; Daniel, Nitin G.; van der Wel, Hanke; Ichikawa, H. Travis; Glushka, John N.; Wells, Lance; Woods, Robert J.; Wood, Zachary A.; West, Christopher M.
  3. JOURNAL OF BIOLOGICAL CHEMISTRY. 2020, JUL 3; 295(27): 9223-9243.
  1. 23.   Characterization of Cationic Bolaamphiphile Vesicles for siRNA Delivery into Tumors and Brain
  2. Kim, Taejin; Viard,Mathias; Afonin, Kirill A; Gupta, Kshitij; Popov, Mary; Salotti,Jacqueline; Johnson,Peter; Linder, Charles; Heldman, Eliahu; Shapiro,Bruce
  3. Molecular therapy. Nucleic acids. 2020, JUN 5; 20: 359-372.
  1. 24.   The quaternary assembly of KRas4B with Raf-1 at the membrane
  2. Jang,Hyunbum; Zhang,Mingzhen; Nussinov,Ruth
  3. Computational and Structural Biotechnology Journal. 2020, Mar 25; 18: 737-748.
  1. 25.   Molecular dynamics based improvement of the solubilizing self-cleavable tag Zbasic-?I-CM application in the preparation of recombinant proteins in Escherichia coli
  2. Luo, Han; Hu, Lifu; Ma,Buyong; Zhao, Meiqi; Luo, Manyu; Deng, Qing; Deng, Shaorong; Ye, Hao; Lin, Tong; Chen, Junsheng; Wang, Tao; Zhu, Jianwei; Lu, Huili
  3. Biochemical and biophysical research communications. 2019, MAY 28; 513(2): 412-418.
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