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  1. 1.   Mechanism of lipid droplet formation by the yeast Sei1/Ldb16 Seipin complex
  2. Klug, Yoel A.; Deme, Justin C.; Corey, Robin A.; Renne, Mike F.; Stansfeld, Phillip J.; Lea, Susan M.; Carvalho, Pedro
  3. Nature Communications. 2021, Oct 8; 12(1):
  1. 2.   Structural basis of antifolate recognition and transport by PCFT
  2. Parker, Joanne L.; Deme,Justin; Kuteyi, Gabriel; Wu, Zhiyi; Huo, Jiandong; Goldman, I. David; Owens, Raymond J.; Biggin, Philip C.; Lea,Susan; Newstead, Simon
  3. Nature. 2021, Jul; 595(7865): 130-134.
  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.   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. 5.   The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-beta Enhanceosome Example
  2. Pan, Y. P.; Nussinov, R.
  3. Plos Computational Biology. 2011, Jun; 7(6): 14.
  1. 6.   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. 7.   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. 8.   Conformational Profile of a Proline-Arginine Hybrid
  2. Revilla-Lopez, G.; Jimenez, A. I.; Cativiela, C.; Nussinov, R.; Aleman, C.; Zanuy, D.
  3. Journal of Chemical Information and Modeling. 2010, Oct; 50(10): 1781-1789.
  1. 9.   Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism
  2. Fishelovitch, D.; Shaik, S.; Wolfson, H. J.; Nussinov, R.
  3. Journal of Physical Chemistry B. 2009 113(39): 13018-13025.
  1. 10.   Computer Simulations of Peptides from the p53 DNA Binding Domain
  2. Khalili, M.; Wales, D. J.
  3. Journal of Chemical Theory and Computation. 2009 5(5): 1380-1392.
  1. 11.   Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer
  2. Saneyoshi, H.; Mazzini, S.; Avino, A.; Portella, G.; Gonzalez, C.; Orozco, M.; Marquez, V. E.; Eritja, R.
  3. Nucleic Acids Research. 2009 37(17): 5589-5601.
  1. 12.   In Silico Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide
  2. Zanuy, D.; Flores-Ortega, A.; Jimenez, A. I.; Calaza, M. I.; Cativiela, C.; Nussinov, R.; Ruoslahti, E.; Aleman, C.
  3. Journal of Physical Chemistry B. 2009 113(22): 7879-7889.
  1. 13.   Asymmetric synthesis of 2,3-dihydro-2-arylquinazolin-4-ones: Methodology and application to a potent fluorescent tubulin inhibitor with anticancer activity
  2. Chinigo, G. M.; Paige, M.; Grindrod, S.; Hamel, E.; Dakshanamurthy, S.; Chruszcz, M.; Minor, W.; Brown, M. L.
  3. Journal of Medicinal Chemistry. 2008 51(15): 4620-4631.
  1. 14.   Intrinsic conformational characteristics of alpha,alpha-diphenylglycine
  2. Casanovas, J.; Zanuy, D.; Nussinov, R.; Aleman, C.
  3. Journal of Organic Chemistry. 2007, Mar; 72(6): 2174-2181.
  1. 15.   Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A
  2. Park, J. G.; Sill, P. C.; Makiyi, E. F.; Garcia-Sosa, A. T.; Millard, C. B.; Schmidt, J. J.; Pang, Y. P.
  3. Bioorganic & Medicinal Chemistry. 2006, Jan; 14(2): 395-408.
  1. 16.   Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method
  2. Nemukhin, A. V.; Grigorenko, B. L.; Rogov, A. V.; Topol, I. A.; Burt, S. K.
  3. Theoretical Chemistry Accounts. 2004 111(1): 36-48.
  1. 17.   Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by Hhal methyltransferase
  2. Horton, J. R.; Ratner, G.; Banavali, N. K.; Huang, N.; Choi, Y.; Maier, M. A.; Marquez, V. E.; Mackerell, A. D.; Cheng, X. D.
  3. Nucleic Acids Research. 2004 32(13): 3877-3886.
  1. 18.   DYNGA: a general purpose QM-MM-MD program. I. Application to water
  2. Parker, C. L.; Ventura, O. N.; Burt, S. K.; Cachau, R. E.
  3. Molecular Physics. 2003 101(17): 2659-2668.
  1. 19.   Metal-dependent inhibition of HIV-1 integrase by beta-diketo acids and resistance of the soluble double-mutant (F185K/C280S)
  2. March, C.; Johnson, A. A.; Karki, R. G.; Pais, G. C. G.; Zhang, X. C.; Cowansage, K.; Patel, T. A.; Nicklaus, M. C.; Burke, T. R.; Pommier, Y.
  3. Molecular Pharmacology. 2003 64(3): 600-609.
  1. 20.   Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations
  2. Li, W.; Ma, B. Y.; Shapiro, B. A.
  3. Nucleic Acids Research. 2003 31(2): 629-638.
  1. 21.   Motion and sorption of gas molecules in poly(octadecyl acrylate)
  2. Zanuy, D.; Zazueta, D. A.; Aleman, C.
  3. Polymer. 2003 44(16): 4735-4745.
  1. 22.   Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop
  2. Li, W.; Ma, B. Y.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2001 19(3): 381-396.
  1. 23.   Explicit and implicit water simulations of a beta-hairpin peptide
  2. Ma, B. Y.; Nussinov, R.
  3. Proteins. 1999 37(1): 73-87.
  1. 24.   Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates
  2. Lii, J. H.; Ma, B. Y.; Allinger, N. L.
  3. Journal of Computational Chemistry. 1999 20(15): 1593-1603.
  1. 25.   A Set of Van Der Waals and Coulombic Radii of Protein Atoms For Molecular and Solvent-Accessible Surface Calculation, Packing Evaluation, and Docking
  2. Li, A. J.; Nussinov, R.
  3. Proteins. 1998 32(1): 111-127.
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