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  1. 1.   Examining the bias-efficiency tradeoff from incorporation of nonconcurrent controls in platform trials: A simulation study example from the adaptive COVID-19 treatment trial
  2. Bonnett,Tyler; Potter, Gail E; Dodd, Lori E
  3. Clinical Trials (London, England). 2025, Feb 08; 17407745251313928.
  1. 2.   Effects of Xylanase A double mutation on substrate specificity and structural dynamics
  2. MacDonald, Meagan E; Wells, Nicholas G M; Hassan,Bakar; Dudley, Joshua A; Walters,Kylie; Korzhnev, Dmitry M; Aramini, James M; Smith, Colin A
  3. Journal of Structural Biology. 2024, Mar 02; 108082.
  1. 3.   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. 4.   HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules
  2. Khatkar, Pooja; Mensah, Gifty; Ning, Shangbo; Cowen, Maria; Kim, Yuriy; Williams, Anastasia; Abulwerdi, Fardokht A; Zhao, Yunjie; Zeng, Chen; Le Grice, Stuart F J; Kashanchi, Fatah
  3. Pharmaceuticals (Basel, Switzerland). 2023, Dec 25; 17(1):
  1. 5.   Multitarget Potential of Phytochemicals from Traditional Medicinal Tree, Terminalia arjuna (Roxb. ex DC.) Wight & Arnot as Potential Medicaments for Cardiovascular Disease: An In-Silico Approach
  2. Kumar, Vikas; Sharma, Nitin; Orfali, Raha; Patel,Chiragkumar; Alnajjar, Radwan; Saini, Rakshandha; Sourirajan, Anuradha; Khosla, Prem Kumar; Dev, Kamal; Perveen, Shagufta
  3. Molecules (Basel, Switzerland). 2023, Jan 20; 28(3):
  1. 6.   Application of Molecular Dynamics to Expand Docking Program's Exploratory Capabilities and to Evaluate Its Predictions
  2. Kasprzak,Wojciech; Shapiro,Bruce
  3. Methods in Molecular Biology (Clifton, N.J.). 2023 2568: 75-101.
  1. 7.   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. 8.   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. 9.   The mechanism of activation of MEK1 by B-Raf and KSR1
  2. Maloney,Ryan; Zhang,Mingzhen; Liu,Yonglan; Jang,Hyunbum; Nussinov,Ruth
  3. Cellular and molecular life sciences : CMLS. 2022, May 04; 79(5): 281.
  1. 10.   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. 11.   Evolution of Thyroglobulin Loop Kinetics in EpCAM
  2. Chen, Serena H.; Bell,David
  3. LIFE-BASEL. 2021, Sep 03; 11(9):
  1. 12.   The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane
  2. Jang,Hyunbum; Smith, Iris Nira; Eng, Charis; Nussinov,Ruth
  3. iScience. 2021, May 21; 24(5):
  1. 13.   The Structural Basis of Akt PH Domain Interaction with Calmodulin
  2. Weako,Jackson; Jang, Hyunbum; Keskin, Ozlem; Nussinov,Ruth; Gursoy, Attila
  3. Biophysical Journal. 2021, May 18; 120(10): 1994-2008.
  1. 14.   What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models
  2. Suarez Alvarez,Ernesto; Wiewiora, Rafal P.; Wehmeyer, Chris; Noe, Frank; Chodera, John D.; Zuckerman, Daniel M.
  3. Journal of chemical theory and computation. 2021, May 11; 17(5): 3119-3133.
  1. 15.   Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
  2. Nguyen, Phuong H.; Ramamoorthy, Ayyalusamy; Sahoo, Bikash R.; Zheng, Jie; Faller, Peter; Straub, John E.; Dominguez, Laura; Shea, Joan-Emma; Dokholyan, Nikolay; De Simone, Alfonso; Ma, Buyong; Nussinov,Ruth; Najafi, Saeed; Ngo, Son Tung; Loquet, Antoine; Chiricotto, Mara; Ganguly, Pritam; McCarty, James; Li, Mai Suan; Hall, Carol; Wang, Yiming; Miller, Yifat; Melchionna, Simone; Habenstein, Birgit; Timr, Stepan; Chen, Jiaxing; Hnath, Brianna; Strodel, Birgit; Kayed, Rakez; Lesne, Sylvain; Wei, Guanghong; Sterpone, Fabio; Doig, Andrew J.; Derreumaux, Philippe
  3. Chemical Reviews. 2021, Feb 24; 121(4): 2545-2647.
  1. 16.   Trastuzumab Blocks the Receiver Function of HER2 Leading to the Population Shifts of HER2-Containing Homodimers and Heterodimers
  2. Zhao, Jun; Mohan, Nishant; Nussinov, Ruth; Ma, Buyong; Wu, Wen Jin
  3. Antibodies. 2021, Jan 12; 10(1):
  1. 17.   SAVI, in silico generation of billions of easily synthesizable compounds through expert-system type rules
  2. Patel,Hitesh; Ihlenfeldt, Wolf-Dietrich; Judson, Philip N; Moroz, Yurii S; Pevzner, Yuri; Peach,Megan; Delannee,Victorien; Tarasova,Nadya; Nicklaus,Marc
  3. Scientific data. 2020, NOV 11; 7(1): 384.
  1. 18.   Computational Investigation of Gantenerumab and Crenezumab Recognition of A beta Fibrils in Alzheimer's Disease Brain Tissue
  2. Chen, Yujie; Wei, Guanghong; Zhao, Jun; Nussinov,Ruth; Ma, Buyong
  3. ACS CHEMICAL NEUROSCIENCE. 2020, OCT 21; 11(20): 3233-3244.
  1. 19.   Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1
  2. Soubias, Olivier; Pant, Shashank; Heinrich, Frank; Zhang,Yue; Roy, Neeladri Sekhar; Li,Jess; Jian, Xiaoying; Yohe, Marielle E; Randazzo, Paul A; Lösche, Mathias; Tajkhorshid, Emad; Byrd,Robert
  3. Science advances. 2020, Sep; 6(40): pii: eabd1882.
  1. 20.   Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD
  2. Travers, Timothy; López, Cesar A; Agamasu, Constance; Hettige, Jeevapani J; Messing,Simon; García, Angel E; Stephen, Andrew G; Gnanakaran, S
  3. Biophysical journal. 2020, AUG 4; 119(3): 525-538.
  1. 21.   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. 22.   Modeling ligand docking to RNA in the design of RNA-based nanostructures
  2. Kasprzak,Wojciech; Ahmed, Nour Ali; Shapiro,Bruce
  3. Current opinion in biotechnology. 2020, JUN; 63: 16-25.
  1. 23.   The Structural Basis of the Farnesylated and Methylated KRas4B Interaction with Calmodulin
  2. Jang,Hyunbum; Banerjee, Avik; Marcus, Kendra; Makowski, Lee; Mattos, Carla; Gaponenko, Vadim; Nussinov,Ruth
  3. Structure (London, England : 1993). 2019, Nov 5; 27(11): 1647-1659.e4.
  1. 24.   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.
  1. 25.   Structures of the PKA RI alpha Holoenzyme with the FLHCC Driver J-PKAc alpha or Wild-Type PKAc alpha
  2. Cao,Baohua; Lu, Tsan-Wen; Martinez Fiesco,Juliana; Tomasini, Michael; Fan,Lixin; Simon, Sanford M.; Taylor, Susan S.; Zhang,Ping
  3. Structure (London, England : 1993). 2019, MAY 7; 27(5): 816-+.
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