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  1. 1.   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. 2.   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. 3.   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. 4.   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. 5.   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. 6.   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. 7.   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. 8.   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. 9.   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. 10.   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. 11.   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. 12.   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. 13.   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-+.
  1. 14.   Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling
  2. Li, Shuai; Jang, Hyunbum; Zhang, Jian; Nussinov, Ruth
  3. Structure . 2018, Mar 6; 26(3): 513-+.
  1. 15.   Anhydrous Monoalkylguanidines in Aprotic and Nonpolar Solvents: Models for Deprotonated Arginine Side Chains in Membrane Environments
  2. Banyikwa, Andrew Toyi; Miller, Stephen; Krebs, Richard A.; Xiao, Yuewu; Carney, Jeffrey M.; Braiman, Mark S.
  3. ACS OMEGA. 2017, OCT; 2(10): 7239-7252.
  1. 16.   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. 17.   Familial Mutations May Switch Conformational Preferences in alpha-Synuclein Fibrils
  2. Xu, Liang; Ma, Buyong; Nussinov, Ruth; Thompson, Damien
  3. ACS CHEMICAL NEUROSCIENCE. 2017, Apr 19; 8(4):
  1. 18.   Protocols for Molecular Dynamics Simulations of RNA Nanostructures.
  2. Kim, Taejin; Kasprzak, Wojciech; Shapiro, Bruce
  3. Methods in molecular biology (Clifton, N.J.). 2017 1632: 33-64.
  1. 19.   Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide
  2. Revilla-Lopez, G.; Torras, J.; Nussinov, R.; Aleman, C.; Zanuy, D.
  3. Physical Chemistry Chemical Physics. 2011, Jun 7; 13(21): 9986-9994.
  1. 20.   Symmetry-Based Self-assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers
  2. Buch, I.; Tsai, C. J.; Wolfson, H. J.; Nussinov, R.
  3. Protein and Peptide Letters. 2011, Apr; 18(4): 362-372.
  1. 21.   Supramolecular complexes of quantum dots and a polyamidoamine (PAMAM)-folate derivative for molecular imaging of cancer cells
  2. Geraldo, D. A.; Duran-Lara, E. F.; Aguayo, D.; Cachau, R. E.; Tapia, J.; Esparza, R.; Yacaman, M. J.; Gonzalez-Nilo, F. D.; Santos, L. S.
  3. Analytical and Bioanalytical Chemistry. 2011, Apr; 400(2): 483-492.
  1. 22.   Molecular-Level Examination of Cu2+ Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer's beta by Solid-State NMR Spectroscopy
  2. Parthasarathy, S.; Long, F.; Miller, Y.; Xiao, Y. L.; McElheny, D.; Thurber, K.; Ma, B. Y.; Nussinov, R.; Ishii, Y.
  3. Journal of the American Chemical Society. 2011, Mar; 133(10): 3390-3400.
  1. 23.   A Simulation Strategy for the Atomistic Modeling of Flexible Molecules Covalently Tethered to Rigid Surfaces: Application to Peptides
  2. Curco, D.; Zanuy, D.; Nussinov, R.; Aleman, C.
  3. Journal of Computational Chemistry. 2011, Mar; 32(4): 607-619.
  1. 24.   Binding of a C-End Rule Peptide to the Neuropilin-1 Receptor: A Molecular Modeling Approach
  2. Haspel, N.; Zanuy, D.; Nussinov, R.; Teesalu, T.; Ruoslahti, E.; Aleman, C.
  3. Biochemistry. 2011, Mar; 50(10): 1755-1762.
  1. 25.   Understanding the effects of carbocyclic sugars constrained to north and south conformations on RNA nanodesign
  2. Kim, T.; Barchi, J. J.; Marquez, V. E.; Shapiro, B. A.
  3. Journal of Molecular Graphics & Modelling. 2011, Feb; 29(5): 624-634.
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