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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
A method to configure protein side-chains from the main-chain trace in homology modelling.
Eisenmenger F, Argos P, Abagyan R. Eisenmenger F, et al. Among authors: abagyan r. J Mol Biol. 1993 Jun 5;231(3):849-60. doi: 10.1006/jmbi.1993.1331. J Mol Biol. 1993. PMID: 8515455
Recognition of distantly related proteins through energy calculations.
Abagyan R, Frishman D, Argos P. Abagyan R, et al. Proteins. 1994 Jun;19(2):132-40. doi: 10.1002/prot.340190206. Proteins. 1994. PMID: 8090707
Homology modeling of GPCRs.
Simms J, Hall NE, Lam PH, Miller LJ, Christopoulos A, Abagyan R, Sexton PM. Simms J, et al. Among authors: abagyan r. Methods Mol Biol. 2009;552:97-113. doi: 10.1007/978-1-60327-317-6_7. Methods Mol Biol. 2009. PMID: 19513644
Flexible protein-ligand docking by global energy optimization in internal coordinates.
Totrov M, Abagyan R. Totrov M, et al. Among authors: abagyan r. Proteins. 1997;Suppl 1:215-20. doi: 10.1002/(sici)1097-0134(1997)1+<215::aid-prot29>3.3.co;2-i. Proteins. 1997. PMID: 9485515
The procedure uses two types of efficient random moves, a pseudobrownian positional move [Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A. ...Chem. 15:488-506, 1994] and a Biased-Probability multitorsion move [Abagyan, R.A., Totrov, M.M. J. Mol. Biol. 235: …
The procedure uses two types of efficient random moves, a pseudobrownian positional move [Abagyan, R.A., Totrov, M.M., Kuznets …
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 …
The contour-buildup algorithm to calculate the analytical molecular surface.
Totrov M, Abagyan R. Totrov M, et al. Among authors: abagyan r. J Struct Biol. 1996 Jan-Feb;116(1):138-43. doi: 10.1006/jsbi.1996.0022. J Struct Biol. 1996. PMID: 8742735
Identification of the individual residues that determine human CD59 species selective activity.
Zhang HF, Yu J, Chen S, Morgan BP, Abagyan R, Tomlinson S. Zhang HF, et al. Among authors: abagyan r. J Biol Chem. 1999 Apr 16;274(16):10969-74. doi: 10.1074/jbc.274.16.10969. J Biol Chem. 1999. PMID: 10196177
In silico discovery of novel retinoic acid receptor agonist structures.
Schapira M, Raaka BM, Samuels HH, Abagyan R. Schapira M, et al. Among authors: abagyan r. BMC Struct Biol. 2001;1:1. doi: 10.1186/1472-6807-1-1. Epub 2001 Jun 4. BMC Struct Biol. 2001. PMID: 11405897 Free PMC article.
Rational discovery of novel nuclear hormone receptor antagonists.
Schapira M, Raaka BM, Samuels HH, Abagyan R. Schapira M, et al. Among authors: abagyan r. Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1008-13. doi: 10.1073/pnas.97.3.1008. Proc Natl Acad Sci U S A. 2000. PMID: 10655475 Free PMC article.
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