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  1. 1.   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. 2.   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. 3.   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. 4.   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. 5.   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. 6.   Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology
  2. Gonzalez-Nilo, F. G.-N. F.; Perez-Acle, T.; Guinez-Molinos, S.; Geraldo, D. A.; Sandoval, C.; Yevenes, A.; Santos, L. S.; Laurie, V. F.; Mendoza, H.; Cachau, R. E.
  3. Biological Research. 2011 44(1): 43-51.
  1. 7.   Polymorphism in Alzheimer A beta Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape
  2. Miller, Y.; Ma, B.; Nussinov, R.
  3. Chemical Reviews. 2010, Aug; 110(8): 4820-4838.
  1. 8.   Atomic-Scale Simulations Confirm that Soluble beta-Sheet-Rich Peptide Self-Assemblies Provide Amyloid Mimics Presenting Similar Conformational Properties
  2. Yu, X.; Wang, J. D.; Yang, J. C.; Wang, Q. M.; Cheng, S. Z. D.; Nussinov, R.; Zheng, J.
  3. Biophysical Journal. 2010, Jan; 98(1): 27-36.
  1. 9.   The Early Years of Retroviral Protease Crystal Structures
  2. Miller, M.
  3. Biopolymers. 2010 94(4): 521-529.
  1. 10.   Computational Validation of Protein Nanotubes
  2. Buch, I.; Brooks, B. R.; Wolfson, H. J.; Nussinov, R.
  3. Nano Letters. 2009 9(3): 1096-1102.
  1. 11.   Polymorphism of Alzheimer's A beta(17-42) (p3) Oligomers: The Importance of the Turn Location and Its Conformation
  2. Miller, Y.; Ma, B. Y.; Nussinov, R.
  3. Biophysical Journal. 2009 97(4): 1168-1177.
  1. 12.   K3 Fragment of Amyloidogenic beta(2)-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis
  2. Mustata, M.; Capone, R.; Jang, H.; Arce, F. T.; Ramachandran, S.; Lal, R.; Nussinov, R.
  3. Journal of the American Chemical Society. 2009 131(41): 14938-14945.
  1. 13.   P53-induced DNA bending: The interplay between p53-ONA and p53-p53 interactions
  2. Pan, Y. P.; Nussinov, R.
  3. Journal of Physical Chemistry B. 2008 112(21): 6716-6724.
  1. 14.   Annular structures as intermediates in fibril formation of Alzheimer A beta(17-42)
  2. Zheng, J.; Jang, H.; Ma, B.; Nussinov, R.
  3. Journal of Physical Chemistry B. 2008 112(22): 6856-6865.
  1. 15.   Modeling the Alzheimer A beta(17-42) fibril architecture: Tight intermolecular sheet-sheet association and intramolecular hydrated cavities
  2. Zheng, J.; Jang, H.; Ma, B.; Tsai, C. J.; Nussinov, R.
  3. Biophysical Journal. 2007, Nov; 93(9): 3046-3057.
  1. 16.   Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations
  2. Grigorenko, B. L.; Nemukhin, A. V.; Shadrina, M. S.; Topol, I. A.; Burt, S. K.
  3. Proteins-Structure Function and Bioinformatics. 2007, Feb; 66(2): 456-466.
  1. 17.   Interaction of protegrin-1 with lipid bilayers: Membrane thinning effect
  2. Jang, H.; Ma, B.; Woolf, T. B.; Nussinov, R.
  3. Biophysical Journal. 2006, Oct; 91(8): 2848-2859.
  1. 18.   Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
  2. Ma, B. Y.; Nussinov, R.
  3. Current Opinion in Chemical Biology. 2006, Oct; 10(5): 445-452.
  1. 19.   The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation
  2. Yingling, Y. G.; Shapiro, B. A.
  3. Journal of Molecular Graphics & Modelling. 2006, Oct; 25(2): 261-274.
  1. 20.   Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure
  2. Zheng, J.; Ma, B. Y.; Nussinov, R.
  3. Physical Biology. 2006, Sep; 3(3): P1-P4.
  1. 21.   From peptide-based material science to protein fibrils: discipline convergence in nanobiology
  2. Zanuy, D.; Nussinov, R.; Aleman, C.
  3. Physical Biology. 2006, Mar; 3(1): S80-S90.
  1. 22.   Insights into amyloid structural formation and assembly through computational approaches
  2. Zanuy, D.; Gunasekaran, K.; Ma, B. Y.; Tsai, H. H.; Tsai, C. J.; Nussinov, R.
  3. Amyloid-Journal of Protein Folding Disorders. 2004, SEP; 11(3): 143-161.
  1. 23.   Modulating functional loop movements: The role of highly conserved residues in the correlated loop motions
  2. Gunasekaran, K.; Nussinov, R.
  3. Chembiochem. 2004 5(2): 224-230.
  1. 24.   Triggering loops and enzyme function: Identification of loops that trigger and modulate movements
  2. Gunasekaran, K.; Ma, B. Y.; Nussinov, R.
  3. Journal of Molecular Biology. 2003 332(1): 143-159.
  1. 25.   EVEBAT: A fast strategy for the examination of the empty space in polymer matrices
  2. Curco, D.; Zanuy, D.; Aleman, C.
  3. Journal of Computational Chemistry. 2003 24(10): 1208-1214.
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