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Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold.
Totrov M, Jiang X, Kong XP, Cohen S, Krachmarov C, Salomon A, Williams C, Seaman MS, Abagyan R, Cardozo T, Gorny MK, Wang S, Lu S, Pinter A, Zolla-Pazner S. Totrov M, et al. Among authors: abagyan r. Virology. 2010 Sep 30;405(2):513-23. doi: 10.1016/j.virol.2010.06.027. Epub 2010 Jul 21. Virology. 2010. PMID: 20663531 Free PMC article.
Homology modeling by the ICM method.
Cardozo T, Totrov M, Abagyan R. Cardozo T, et al. Among authors: abagyan r. Proteins. 1995 Nov;23(3):403-14. doi: 10.1002/prot.340230314. Proteins. 1995. PMID: 8710833
Estimating local backbone structural deviation in homology models.
Cardozo T, Batalov S, Abagyan R. Cardozo T, et al. Among authors: abagyan r. Comput Chem. 2000 Jan;24(1):13-31. doi: 10.1016/s0097-8485(99)00044-3. Comput Chem. 2000. PMID: 10642877 Free article.
The locations and extent of spatial deviations in the backbone between correctly aligned homologous protein structures remained very poorly estimated however, and these errors were the cause of errant loop predictions [Abagyan, R., Batalov, S., Cardozo, T., Totrov, …
The locations and extent of spatial deviations in the backbone between correctly aligned homologous protein structures remained very poorly …
Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search.
Abagyan R, Batalov S, Cardozo T, Totrov M, Webber J, Zhou Y. Abagyan R, et al. Proteins. 1997;Suppl 1:29-37. doi: 10.1002/(sici)1097-0134(1997)1+<29::aid-prot5>3.3.co;2-4. Proteins. 1997. PMID: 9485492
For all five low identity targets: (i) our starting models were improved by the Internal Coordinate Mechanics (ICM) energy optimization, (ii) the refined models were consistently better than those built with the automatic SWISS-MODEL program, and (iii) the refined models differed …
For all five low identity targets: (i) our starting models were improved by the Internal Coordinate Mechanics (ICM) energy optimization, (ii …
Long pentraxins: an emerging group of proteins with diverse functions.
Goodman AR, Cardozo T, Abagyan R, Altmeyer A, Wisniewski HG, Vilcek J. Goodman AR, et al. Among authors: abagyan r. Cytokine Growth Factor Rev. 1996 Aug;7(2):191-202. doi: 10.1016/1359-6101(96)00019-6. Cytokine Growth Factor Rev. 1996. PMID: 8899296 Review.
Spatial chemical distance based on atomic property fields.
Grigoryan AV, Kufareva I, Totrov M, Abagyan RA. Grigoryan AV, et al. Among authors: abagyan ra. J Comput Aided Mol Des. 2010 Mar;24(3):173-82. doi: 10.1007/s10822-009-9316-x. Epub 2010 Mar 13. J Comput Aided Mol Des. 2010. PMID: 20229197 Free PMC article.
347 results