E. Alexov and M. Gunner. Modeling the First Electron Transfer from QA to QB. Molecular Bioenergetics: Simulations of Electron, Proton, and Energy Transfer, Amer Chemical Society, issue 883, pages 93, 2004.

E. Alexov and M. Gunner. Modeling the First Electron Transfer from QA to QB in Reaction Center Proteins from Rb. sphaeroides. 2004.

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.

A. Shosheva, A. Donchev, M. Dimitrov, I. Zlatanov, G. Toromanov, V. Getov, and E. Alexov. Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, Elsevier, volume 1698, issue 1, pages 67-75, 2004.

E. Alexov. Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein--inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin--pepstatin complexes. Proteins: Structure, Function, and Bioinformatics, Wiley Online Library, volume 56, issue 3, pages 572-584, 2004.

E. Alexov. Numerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure. European Journal of Biochemistry, Blackwell Science Ltd Oxford, UK, volume 271, issue 1, pages 173-185, 2004.