| 1992 | ||
| 19. | Abagyan, R.A., and Argos, P. (1992). Optimal Protocol and Trajectory Visualization for Conformational Searches of Peptides and Proteins. J. Mol. Biol., 225, 519-532 [Abs.] | |
| 22. | Petukhov, M.G., Dorofeev, V.E., Abagyan, R.A., Mazur, A.K. (1992). Global optimization of the conformational energy of oligopeptides using a tunnel algorithm. Biofizika, 37, 226-230 [Abs.] | |
| 1993 | ||
| 23. | Abagyan, R.A. (1993). Towards protein folding by global energy optimization. FEBS Letters, 325,17-22 [Abs.] | |
| 25. | Eisenmenger, F., Argos, P., and Abagyan, R.A., (1993). A method to configure protein side-chains from the mainchain trace in homology modeling. J. Mol. Biol., 231, 849-860 [Abs.] | |
| 27. | Kuznetsov, D.A., and Abagyan, R.A. (1993). A technique for identifying atoms from a screen image. J. Mol. Graph., 11, 245-247 [Abs.] | |
| 1994 | ||
| 30. | Abagyan, R.A., and Totrov, M.M. (1994). Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins. J. Mol. Biol., 235, 983-1002 [Abs.] | |
| 33. | Abagyan, R.A., Totrov, M.M., and Kuznetsov, D.A. (1994). ICM: a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comp. Chem., 15, 488-506 [Abs.] | |
| 34. | Totrov, M.M., and Abagyan, R.A. (1994). Efficient parallelization of the energy, surface and derivative calculations for internal coordinate mechanics. J. Comp. Chem., 15, 1105-1112 [Abs.] | |
| 1996 | ||
| 38. | Totrov, M.M., and Abagyan, R.A. (1996). The Contour-Buildup Algorithm to Calculate the Analytical Molecular Surface. J. Struct. Biol., 116, 138-143 [Abs.]-[PDF] | |
| 39. | Chalikian, T.V., Totrov, M.M., Abagyan, R.A., Breslauer, K.J. (1996). The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. J. Mol. Biol., 260, 588-603 [Abs.]-[PDF] | |
| 1997 | ||
| 46. | Abagyan, R., and Totrov, M. (1997). Contact Area Difference (CAD): A robust measure to evaluate accuracy of protein models. J. Mol. Biol., 268, 678-285 [Abs.]-[PDF] | |
| 51. | Abagyan, R. (1997). Protein structure prediction by global energy optimization. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, (van Gunsteren, W.F., et al., eds.). 3, 363-394 [Abs.]-[PDF] | |
| 52. | Rashin, A.A., Rashin, B.H., Rashin A., Abagyan, R. (1997). Evaluating the energetics of empty cavities and internal mutations in proteins. Protein Science, 6, 2143-2158 [Abs.] | |
| 1999 | ||
| 67. | Zhou, Y., and Abagyan, R. (1999). Efficient stochastic global optimization for protein structure prediction. Rigidity Theory and Application (M.F. Thorpe & P.M. Duxbury eds.), 345-356 [Abs.] | |
| 2000 | ||
| 68. | Cardozo, T., Batalov, S., and Abagyan, R. (2000). Estimating local backbone structural deviation in homology models. Estimating local backbone structural deviation in homology models. Computers & Chemistry . Jan 24(1), 13-31 [Abs.]-[PDF] | |
| 2001 | ||
| 79. | Totrov, M., and Abagyan, R. (2001). Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide. Biopolymers 2001;60(2):124-33 [Abs.]-[PDF] |