E. Alexov and B. Honig. Structural and Energetic Basis of Molecular Recognition. Handbook of Cell Signaling, Academic Press, pages 11-13, 2010.

M. Kosloff, E. Alexov, V. Y. Arshavsky, and B. Honig. Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. Journal of Biological Chemistry, Elsevier, volume 283, issue 45, pages 31197-31207, 2008.

C. Bertonati, B. Honig, and E. Alexov. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophysical journal, Elsevier, volume 92, issue 6, pages 1891-1899, 2007.

C. L. Tang, E. Alexov, A. M. Pyle, and B. Honig. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. Journal of molecular biology, Academic Press, volume 366, issue 5, pages 1475-1496, 2007.

J. Zhu, E. Alexov, and B. Honig. Comparative study of generalized Born models: Born radii and peptide folding. The Journal of Physical Chemistry B, ACS Publications, volume 109, issue 7, pages 3008-3022, 2005.

C. L. Tang, D. Petrey, M. Fasnacht, M. Kosloff, E. Alexov, and B. Honig. Use of limited suboptimal alignment in homology modeling. Poster presented at 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2004.

E. Alexov and B. Honig. Proton uptake/release induced by protein-inhibitor association. Application to pepstatin and plasmepsin, cathepsin D and endothiapepsin complexes. BIOPHYSICAL JOURNAL, volume 84, issue 2, pages 505A-505A, 2003.

C. L. Tang, L. Xie, I. Y. Koh, S. Posy, E. Alexov, and B. Honig. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. Journal of molecular biology, Elsevier, volume 334, issue 5, pages 1043-1062, 2003.

W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig. Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method. J Comp Chem, volume 23, pages 128-137, 2002.

C. Tang, E. Alexov, A. Pyle, and B. Honig. Perturbations of pKa in RNA structures: A survey using a Monte Carlo application of the NLPB equation. BIOPHYSICAL JOURNAL, volume 82, issue 1, pages 131A-131A, 2002.

E. Alexov and B. Honig. The origins of pH dependent effects on protein stability: Applications to proteases. Biophysical Journal, volume 82, issue 1, pages 474A-474A, 2002.

W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. Journal of computational chemistry, Wiley Online Library, volume 23, issue 1, pages 128-137, 2002.

W. Rocchia, E. Alexov, and B. Honig. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions (vol 105B, pg 6507, 2001). Journal of Physical Chemistry B, American Chemical Society (ACS), volume 105, issue 28, pages 6754-6754, 2001.

W. Rocchia, E. Alexov, and B. Honig. ADDITIONS AND CORRECTIONS-Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions. Journal of Physical Chemistry B-Condensed Phase, Washington, DC: American Chemical Society, c1997-, volume 105, issue 28, pages 6754, 2001.

W. Rocchia, E. Alexov, and B. Honig. Extending the applicability of the nonlinear Poisson- Boltzmann equation: multiple dielectric constants and multivalent ions. The Journal of Physical Chemistry B, American Chemical Society, volume 105, issue 28, pages 6507-6514, 2001.