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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.   AI-driven drug repurposing and binding pose meta dynamics identifies novel targets for monkeypox virus
  2. Patel,Chiragkumar; Mall, Raghvendra; Bensmail, Halima
  3. Journal of Infection and Public Health. 2023, Mar 15; 16(5): 799-807.
  1. 10.   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. 11.   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. 12.   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. 13.   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. 14.   Insights into HIV-1 Transmission Dynamics Using Routinely Collected Data in the Mid-Atlantic United States
  2. Kassaye, Seble G; Grossman, Zehava; Vengurlekar, Priyanka; Chai, William; Wallace, Megan; Rhee, Soo-Yon; Meyer, William A; Kaufman, Harvey W; Castel, Amanda; Jordan, Jeanne; Crandall, Keith A; Kang, Alisa; Kumar, Princy; Katzenstein, David A; Shafer, Robert W; Maldarelli,Frank
  3. Viruses. 2022, Dec 25; 15(1):
  1. 15.   Computational investigation of natural compounds as potential main protease (Mpro) inhibitors for SARS-CoV-2 virus
  2. Patel,Chiragkumar; Jani, Siddhi P; Prasanth Kumar, Sivakumar; Modi, Krunal M; Kumar, Yogesh
  3. Computers in Biology and Medicine. 2022, Nov 18; 151(Pt A): 106318.
  1. 16.   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. 17.   Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA
  2. LeBlanc, Regan M; Kasprzak,Wojciech; Longhini, Andrew P; Olenginski, Lukasz T; Abulwerdi, Fardokht; Ginocchio, Stefano; Shields, Brigit; Nyman, Julie; Svirydava, Maryia; Del Vecchio, Claudia; Ivanic,Joseph; Schneekloth,Jay; Shapiro, Bruce A; Dayie, Theodore Kwaku; Le Grice,Stuart
  3. Journal of Biomolecular Structure & Dynamics. 2022, Jun 22; 40(20): 9761-9773.
  1. 18.   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. 19.   Conformational dynamics of the hepatitis B virus pre-genomic RNA on multiple time scales: implications for viral replication
  2. Olenginski, Lukasz T; Kasprzak,Wojciech; Bergonzo, Christina; Shapiro,Bruce; Dayie, Theodore K
  3. Journal of Molecular Biology. 2022, May 17; 434(18): 167633.
  1. 20.   Metabolic Profile, Biotransformation, Docking Studies and Molecular Dynamics Simulations of Bioactive Compounds Secreted by CG3 Strain
  2. Messaoudi, Omar; Sudarman, Enge; Patel,Chiragkumar; Bendahou, Mourad; Wink, Joachim
  3. Antibiotics (Basel, Switzerland). 2022, May 13; 11(5):
  1. 21.   A phase 1 and pharmacodynamic study of chronically-dosed, single-agent veliparib (ABT-888) in patients with BRCA1- or BRCA2-mutated cancer or platinum-refractory ovarian or triple-negative breast cancer
  2. Manzo, Julia; Puhalla, Shannon; Pahuja, Shalu; Ding, Fei; Lin, Yan; Appleman, Leonard; Tawbi, Hussein; Stoller, Ronald; Lee, James J; Diergaarde, Brenda; Kiesel, Brian F; Yu, Jing; Tan, Antoinette R; Belani, Chandra P; Chew, Helen; Garcia, Agustin A; Morgan, Robert J; Wahner Hendrickson, Andrea E; Visscher, Daniel W; Hurley, Rachel M; Kaufmann, Scott H; Swisher, Elizabeth M; Oesterreich, Steffi; Katz, Tiffany; Ji,Jay; Zhang, Yiping; Parchment, Ralph E; Chen, Alice; Duan, Wenrui; Giranda, Vincent; Shepherd, Stacie P; Ivy, S Percy; Chu, Edward; Beumer, Jan H
  3. Cancer Chemotherapy and Pharmacology. 2022, Apr 18; 89(5): 721-735.
  1. 22.   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. 23.   Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach
  2. Smith, Kyle P; Lee, Woonghee; Tonelli, Marco; Lee, Yeongjoon; Light, Samuel H; Cornilescu,Gabriel; Chakravarthy, Srinivas
  3. Protein Science : a Publication of the Protein Society. 2022, Feb 08; 31(5):
  1. 24.   Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
  2. Ingólfsson, Helgi I; Neale, Chris; Carpenter, Timothy S; Shrestha,Rebika; López, Cesar A; Tran, Timothy H; Oppelstrup, Tomas; Bhatia, Harsh; Stanton, Liam G; Zhang, Xiaohua; Sundram, Shiv; Di Natale, Francesco; Agarwal, Animesh; Dharuman, Gautham; Kokkila Schumacher, Sara I L; Turbyville,Tommy; Gulten, Gulcin; Van, Que N; Goswami, Debanjan; Jean-Francois, Frantz; Agamasu, Constance; Chen, De; Hettige, Jeevapani J; Travers, Timothy; Sarkar, Sumantra; Surh, Michael P; Yang, Yue; Moody, Adam; Liu, Shusen; Van Essen, Brian C; Voter, Arthur F; Ramanathan, Arvind; Hengartner, Nicolas W; Simanshu, Dhirendra K; Stephen, Andrew G; Bremer, Peer-Timo; Gnanakaran, S; Glosli, James N; Lightstone, Felice C; McCormick, Frank; Nissley, Dwight V; Streitz, Frederick H
  3. Proceedings of the National Academy of Sciences of the United States of America. 2022, Jan 04; 119(1):
  1. 25.   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.
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