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  1. 1.   Optimization of multiple-sequence alignment based on multiple-structure alignment
  2. Shatsky, M.; Nussinov, R.; Wolfson, H. J.
  3. Proteins-Structure Function and Bioinformatics. 2006, JAN 1; 62(1): 209-217.
  1. 2.   Potent antiviral activity of North-methanocarbathymidine against Kaposi's sarcoma-associated herpesvirus
  2. Zhu, W. M.; Burnette, A.; Dorjsuren, D.; Roberts, P. E.; Huleihel, M.; Shoemaker, R. H.; Marquez, V. E.; Agbaria, R.; Sei, S.
  3. Antimicrobial Agents and Chemotherapy. 2005, DEC; 49(12): 4965-4973.
  1. 3.   Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies
  2. Inbar, Y.; Benyamini, H.; Nussinov, R.; Wolfson, H. J.
  3. Physical Biology. 2005, DEC; 2(4, Sp. Iss.): S156-S165.
  1. 4.   Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta 2-microglobulin amyloidosis
  2. Benyamini, H.; Gunasekaran, K.; Wolfson, H.; Nussinov, R.
  3. Biochimica Et Biophysica Acta-Proteins and Proteomics. 2005, NOV 10; 1753(1): 121-130.
  1. 5.   Understanding how the herpes thymidine kinase orchestrates optimal sugar and nucleobase conformations to accommodate its substrate at the active site: A chemical approach
  2. Marquez, V. E.; Choi, Y.; Comin, M. J.; Russ, P.; George, C.; Huleihel, M.; Ben-Kasus, T.; Agbaria, R.
  3. Journal of the American Chemical Society. 2005, NOV 2; 127(43): 15145-15150.
  1. 6.   Assortative mating in Drosophila adapted to a microsite ecological gradient
  2. Singh, S. R.; Rashkovetsky, E.; Iliadi, K.; Nevo, E.; Korol, A.
  3. Behavior Genetics. 2005, NOV; 35(6): 753-764.
  1. 7.   ARTS: alignment of RNA tertiary structures
  2. Dror, O.; Nussinov, R.; Wolfson, H.
  3. Bioinformatics. 2005, SEP; 21(Suppl. 2): 47-53.
  1. 8.   Metabolic activation of zebularine, a novel DNA methylation inhibitor, in human bladder carcinoma cells
  2. Ben-Kasus, T.; Ben-Zvi, Z.; Marquez, V. E.; Kelley, J. A.; Agbaria, R.
  3. Biochemical Pharmacology. 2005, JUL 1; 70(1): 121-133.
  1. 9.   Effect of CD8(+) lymphocyte depletion on virus containment after simian immunodeficiency virus SIVmac251 challenge of live attenuated SIVmac239 Delta 3-vaccinated rhesus macaques
  2. Schmitz, J. E.; Johnson, R. P.; McClure, H. M.; Manson, K. H.; Wy, M. S.; Kuroda, M. J.; Lifton, M. A.; Khunkhun, R. S.; McEvers, K. J.; Gillis, J.; Piatak, M.; Lifson, J. D.; Grosschupff, G.; Racz, P.; Tenner-Racz, K.; Rieber, E. P.; Kuus-Reichel, K.; Gelman, R. S.; Letvin, N. L.; Montefiori, D. C.; Ruprecht, R. M.; Desrosiers, R. C.; Reimann, K. A.
  3. Journal of Virology. 2005, JUL; 79(13): 8131-8141.
  1. 10.   Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
  2. Tsai, H. H.; Reches, M.; Tsai, C. J.; Gunasekaran, K.; Gazit, E.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, JUN 7; 102(23): 8174-8179.
  1. 11.   Prediction of multimolecular assemblies by multiple docking
  2. Inbar, Y.; Benyamini, H.; Nussinov, R.; Wolfson, H. J.
  3. Journal of Molecular Biology. 2005, JUN 3; 349(2): 435-447.
  1. 12.   Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach
  2. Keskin, O.; Ma, B. Y.; Rogale, K.; Gunasekaran, K.; Nussinov, R.
  3. Physical Biology. 2005, JUN; 2(2): S24-S35.
  1. 13.   Preface - Protein-protein interactions: principles and prediction
  2. Nussinov, R.; Tsai, C. J.
  3. Physical Biology. 2005, JUN; 2(2):
  1. 14.   The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins
  2. Ma, B. Y.; Pan, Y. P.; Gunasekaran, K.; Keskin, O.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Physical Biology. 2005, JUN; 2(2): S56-S66.
  1. 15.   Dynamics of the antiviral activity of N-methanocarbathymidine against herpes simplex virus type 1 in cell culture
  2. Huleihel, M.; Talishanisky, M.; Ford, H.; Marquez, V. E.; Kelley, J. A.; Johns, D. G.; Agbaria, R.
  3. International Journal of Antimicrobial Agents. 2005, MAY; 25(5): 427-432.
  1. 16.   From structure to function: Methods and applications
  2. Wolfson, H. J.; Shatsky, M.; Schneidman-Duhovny, D.; Dror, O.; Shulman-Peleg, A.; Ma, B. Y.; Nussinov, R.
  3. Current Protein & Peptide Science. 2005, APR; 6(2): 171-183.
  1. 17.   Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface
  2. Ma, B. Y.; Pan, Y. P.; Gunasekaran, K.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005, MAR 15; 102(11): 3988-3993.
  1. 18.   How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues
  2. Haliloglu, T.; Keskin, O.; Ma, B. Y.; Nussinov, R.
  3. Biophysical Journal. 2005, MAR; 88(3): 1552-1559.
  1. 19.   In the quest for stable rescuing mutants of p53: Computational mutagenesis of flexible loop L1
  2. Pan, Y. P.; Ma, B. Y.; Venkataraghavan, R. B.; Levine, A. J.; Nussinov, R.
  3. Biochemistry. 2005, FEB 8; 44(5): 1423-1432.
  1. 20.   A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: A single beta-sheet model with a small hydrophobic core
  2. Haspel, N.; Zanuy, D.; Ma, B. Y.; Wolfson, H.; Nussinov, R.
  3. Journal of Molecular Biology. 2005, FEB 4; 345(5): 1213-1227.
  1. 21.   Regulation of raf-1 by direct feedback phosphorylation
  2. Dougherty, M. K.; Muller, J.; Ritt, D. A.; Zhou, M.; Zhou, X. Z.; Copeland, T. D.; Conrads, T. P.; Veenstra, T. D.; Lu, K. P.; Morrison, D. K.
  3. Molecular Cell. 2005, JAN 21; 17(2): 215-224.
  1. 22.   Discovery of protein substructures in EM maps
  2. Lasker, K.; Dror, O.; Nussinov, R.; Wolfson, H.
  3. Algorithms in bioinformatics. 2005; 3692 : 423-434.
  1. 23.   MAPPIS: Multiple 3D alignment of protein-protein interfaces
  2. Shulman-Peleg, A.; Shatsky, M.; Nussinov, R.; Wolfson, H. J.
  3. Computational Life Sciences. 2005; 3695 : 91-103.
  1. 24.   Multiple docking for protein structure prediction
  2. Inbar, Y.; Wolfson, H. J.; Nussinov, R.
  3. International Journal of Robotics Research. 2005, FEB-MAR; 24(2-3): 131-150.
  1. 25.   Quantitative kinetic analysis of the bacteriophage lambda genetic network
  2. Kobiler, O.; Rokney, A.; Friedman, N.; Court, D. L.; Stavans, J.; Oppenheim, A. B.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2005 102(12): 4470-4475.
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