PublicationsAlexov lab: Computational Biophysics and Bioinformatics

  1. Teng S.,Madej T.,Panchenko A.,  and Alexov E.     " Modelling Effects Of the Human Single Nucleotide Polymorphisms On Protein-Protein Interactions”  Biophysical Journal 96 (2009),2178-2188  pdf 

  2. Talley Kemper,Ng Carmen,Snoppell Michael,Kundrotas Petras and Alexov E.     "On the electrostatic component of protein-protein binding free energy ”  PMC Biophysics 2008,1:2  1-23  pdf 

  3. Kosloff M.,Alexov E.,ArshavskyY. and Hong B.     "Electrostatic and Lipid Anchor Contributions to the Interaction of Transducin with Memebrane”  The Journal of Biological Chemistry 283(2008)  31197-31207  pdf 

  4. Mitra R.,Shyam R.,Mitra I.,Mitra.Miteva M,Alexov E."Calculating the Protanation States of Proteins and Small Molecules: Implications to Ligand-Receptor Interactions ” Current Computer-Aided Drug Design 4(2008) pdf           

  5. Editorial   Current Pharmaceutical Biotechnology (2008) 9:55-56 pdf  

  6.  Petras J. Kundrotas,Marc F. Lensink,Alexov, E.   "Homology-based  modeling   of 3D structures of protein-protein complexes using alignments of modified sequence profiles ”  International Journal of Biological Macromolecules 43(2008)  198-208 pdf 

  7. Teng S., Michonova-Alexova E and Alexov, E.  "Approaches and Resources for prediction of the Effects of Non-Synonymous Single Nucleotide Polymorphism on Protein Function and Intearctions”  Current Pharmaceutical Biotechnology (2008) 9:123-133  pdf

  8. Talley,K., Kundrotas,P.J.,and Alexov, E. “ "Modelling Salt Dependence of Protein-Protein Association:Linear vs Non-Linear Poisson-Bolzmann Equation”  Comm. in Computational Physics (2008) 3:1071-1086-625 pdf

  9. Miteva, A.Maria, Alexov , Emil, Villoutreix, Bruno.O  "Protein Structure Analysis Online”  Current Protocols in Protein Science (2007)  2:13:1-23 pdf

  10. Kundrotas, P.J. and Alexov, E. “Predicting interacting and interfacial residues using continuous sequence segments” Int. J. Biological Macromolecules.(2007) 41:615-625 pdf .

  11. Brook, K., Talley, K., Coley, K., Kundrotas P.J. and Alexov, E. “Optimization of electrostatic interactions in protein-protein complexes”  Biophys. J. (2007) 93:3340-3352  pdf

  12. Kundrotas, P.J., Georgieva, P.,Shosheva, A., Christova, P., and Alexov, E. “Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families ”” J. Bioinformatics and Comput Biol .(2007) 5:693-715 pdf

  13.  Ofiteru, A., Bucurenci, N., Alexov, E., Bertrand, T., Briozzo, P., Munier-Lehmann, H. and Gilles, A.-M.”Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase”, FEBS Journal  (2007) 274, 3363–3373 pdf

  14.  Kundrotas, P.J., Georgieva, P.,Shosheva, A., Christova, P., and Alexov, E. “BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families ” Int.J. Biological Macromolecules (2007) 41, 114-119. pdf

  15.  Tang, C.L..., Alexov, E., Pyle, A.M. and Honig, B. “Calculations of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides” J. Mol.Biol.. (2007), 366,:1475—1498. pdf

  16.  Isvoran, A.., Craescu, C.T.. and Alexov, E. “Electrostatic control of the overall shape of calmodium: numerical calculations” Eur. Biophys. J. (2007), doi 10.1007/s00249-006-0123-1. pdf

  17.  Bertonati, C., Honig, B. and Alexov, E. “Poisson-Boltzmann Calculations of Nonspecific Salt Effects on Protein-Protein Binding Free Energies” Biophys. J.  (2007) 92:1891-1899. pdf

  18.  Kundrotas, P.J. and Alexov, E. “Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives” BMC Bioinformatics (2006) 7:503. pdf

  19.  Kundrotas, P.J. and Alexov, E.. “PROTCOM: searchable database of protein complexes enhanced with domain-domain structures” Nucleic Acids Research (2007) 35, D575-D579 pdf.

  20.  Kundrotas, P.J. and Alexov, E. “Predicting 3D structures of transient protein-protein complexes by homology” Biochim et Biophys Acta—Proteins and Proteomics (2006) 1764, 1498-1511 pdf..

  21.  Kundrotas, P.J. and Alexov, E. “Electrostatic properties of protein-protein complexes” Biophys. J (2006), 91, 1724-1736. pdf

  22.  Wu, Y., Hudson, J.G., Lu, Q., Moore, J.M., Mount, A.S., Rao, A.M., Alexov, E. and Ke, P.C. “Coating single-walled carbon nanotubes with phospholipids” J.Phys.Chem B (2006), 110, 2475-2478.

  23.  Grey, M.J., Tang, Y., Alexov, E., McKnight, J., Raleigh, D.P., and Palmer III, A.G. “Characterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: Contribution of His41 to the pH-dependent stability of the N-terminal subdomain” J Mol Biol (2006), 355, 1078-1094. pdf

  24.  Shosheva, A., Donchev, A., Dimitrov, M., Kostov, G., Toromanov, G., Getov, V and E. Alexov “Comparative study of the stability of poplar plastocyanin isoforms” BBA (2005), 1748, 116-127. pdf

  25.  Zhu, J., Alexov, E. and B. Honig “Comparative Study of Generalized Born Models: Born Radii and Peptide Folding” J. Phys. Chem. B (2005) 109, 3008-3022. pdf

  26.  Alexov, E. “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 (2004), 56, 572-584.. pdf

  27.  Tang C., Xie L., Koh I., Posy S., Alexov E. and Honig B. “On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles” J. Mol. Biol. (2003), 334, 1043-1062. .pdf

  28.  Shosheva, A., Donchev, A., Dimitrov, M., Zlatanav, I., Toromanov, G., Getov, V. and Alexov, E. “Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity” BBA (2004), 1698, 67-75. pdf

  29.  Alexov, E. “Numerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure” Eur. J. Biochem. (2004), 271, 173-185.. pdf

  30.  Petrey D., Xiang Z., Tang C., Xie. L., Gimpelev M., Mitros T., Soto C., Golgsnith-Fischman S., Kernytsky A., Schlessinger A., Koh I., Alexov E. and Honig B.  “Using Multiple Structure Alignment, Fast Model Building, and Energetic Analysis in Fold Recognition and Homology Modeling” Proteins (2003), 53, 430-435. pdf

  31.  Alexov, E. and Honig, B. “Structural and Energetic Basis of Molecular Recognition” in Handbook of Cell Signaling (2002), R. Bradshaw and E. A. Dennis, Editors, Academic Press, San Diego, CA. p.11-13.

  32.  Alexov, E. “Role of the Protein Side-Chain Fluctuations on the Strength of Pair-Wise Electrostatic Interactions: Comparing Experimental with Computed pKa’s”, Proteins (2003), 50, 94-103. pdf

  33.  Georgescu, R., Alexov, E. and Gunner M. “Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKa’s in Proteins” Biophys. J. (2002), 83, 1731-1748. pdf

  34.  J. Tandory, P. Maroti, E. Alexov, P. Sebban and L. Baciou “Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides” PNAS (2002), 99, 6702-6706.. pdf

  35.  J. Tandory, L. Baciou, E. Alexov, P. Maroti, M. Schiffer, D. Hanson and P. Sebban “Revealing the Involvement of Extended Hydrogen Bond Networks in the Cooperative Function between Distant Sites in Bacterial Reaction Center”, J. Biol. Chem. (2001), 276, 45513-45515. pdf

  36.  Rocchia, W., Sridharan, S., Nicholls, A., Alexov, E., Chiabrera, A. and Honig, B. “ Rapid grid-based Construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: application to the molecular systems and geometrical objects”, J. Comp. Chem. (2002), 23, 128-137. pdf

  37.  Rocchia, W., Alexov, E. and Honig, B. “Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions”, J. Phys. Chem. (2001), 105, 6507-6514 .pdf

  38.  Alexov, E., Valerio-Lepinies, M., Baciou, L., Schiffer, M., Hadson, D.K, Sebban, P. and Gunner, M. "Modeling the effects of mutations within QB pocket in reaction center proteins", Biochemistry  (2000), 39, 5940-5952. pdf

  39.  Gunner, M. and Alexov, E." A pragmatic approach to structure based calculations of coupled proton and electron transfer in proteins", BBA (2000), 44819 , 63-87. pdf

  40.  Alexov, E. and Gunner, M. "Calculating protein and proton motions coupled to electron transfer: The electron transfer from QA to QB in photosynthetic reaction centers from Rb. Sphaeroides", Biochemistry, (1999), 38 (26) 8253-8270. pdf

  41.  Miteva, M., Alexov , E. and Atanasov, B. Numerical simulation of aldolase tetramer stability, Eur. Biophys. J.  (1998), 28, 67-73. pdf

  42.  Gunner, R., Alexov, E., Torres E and Lipovaca S. The importance of the protein in controlling the electrochemistry of heme metalloproteins. Methods of calculation and analysis. JBPC  (1997), 2, 126-134

  43.  Gunner, M.R. and Alexov, E. (1997) The role of the protein in modulating cofactor electrochemistry in proteins: The calculation of electrostatic forces. Molecular modeling and dynamics of bioinorganic systems. Dordrecht, Kluwer. (L. Banci and P. Comba ed.) 361-390.

  44.  Alexov, E.G. & Gunner, M.R. "Including protein conformational flexibility into the calculation of  pH-dependent protein properties", Biophys. J.  (1997) 74, 2075-2093 pdf

  45.  Alexov, E. ,Atanasov, B. "Selective absorption of radio frequency energy due to collective motion of charged domains: Case of lysozyme crystal",  J. Biomolecular Structure and Dynamics, (1995), 13 (2), 219.

  46.  Ohshima, H., Mishonova, E. and Alexov, E. Electrostatic interactions between two charged spheres, Biophysical Chemistry (1996), 57, 189- 203.

  47.  Alexov, E. "High-frequency backward waves in longitudinally magnetized gyrotropic waveguides", Contrib. Plasma Phys. (1995),  35, 23-32.

  48.  Alexov, E. , Atanasov, B. and Ueki, T. "Anisotropic behavior of the pH-dependence part of Young's modulus in a lysozyme triclinic crystal", Biopolymers (1994), 33,513 - 522.

  49.  Alexov, E. and Mishonova, E. "Modeling of electrostatic potential created by spherical molecule" J. Macromolecular Science: Physics (1994), B33, 21-36.

  50.  Alexov, E. and Atanasov, B. "Analysis of electrostatic interactions in ribonuclease A monoclinic crystal" Biochimica et Biophysica Acta, (1994), 1206, 55-62.

  51.  Alexov, E.,, Ivanov, S.T. and Kapchinskii, M.I, "Rejection band in waveguide filled with cold magnetoactive plasma", Jpn. J. Appl. Phys. (1994),33, 5A, 2730-2734

  52.  Ivanov S.T., Ivanova K.M. and Alexov E.G., "Polaritons along the interface between an anysotropic semiconductor and a metallic screen", Physica Scripta, (1994), 48, 568.

  53.  Ivanov S.T. and Alexov E.G., "Cherenkov generation of rayleigh electromagnetic wave in a gyrotropic plasma waveguide", Nuclear Instruments & Methods in Physics Research (1994), A 341, 109.

  54.  Ivanov S.T., Ivanova .M., Alexov E.G., " Rayleigh surface waves along the boundary between a plasma and metallic screen", J. Plasma Phys., (1993), 49, 227.

  55.  Alexov E.G., Ivanov S.T., " Nonreciprocal effects in a plasma waveguide", IEEE Trans. Plasma Sci. , (1993), 21, #2 , 254 - 257.

  56.  Alexov E.G. , "An additional solution of the waveguide problem for a waveguide partially filled with a magnetoactive semiconductor plasma", Phys. Scripta, (1992), 46, 429.

  57.  Alexov E.G., Ivanov S.T., "Anysotropic HE mode in a plasma waveguide",  Sov. J. Plasma Phys. (USA), 1990, 16, 493.

  58.  Ivanov S.T., Alexov E.G., Bogdanov A.T., Malinov P.N., "Surface wave evolution in a waveguide with an axial plasma column upon changing the external magnetic field", Plasma Phys. Control. Fusion, (1990), 32 , 791.

  59.  Ivanov S.T., Alexov E.G., Malinov E.G., Phys. Scripta, (1990), 42, 452.

  60.  Ivanov S.T., Bogdanov A.T., Alexov E.G., "A new family of electromagnetic waves in a waveguide filled with magnetoactive semiconductor plasma", Phys. Scripta, (1990), 42, 458.

  61.  Ivanov S.T., Alexov E.G., "Electromagnetic waves in a homogeneously plasma-filled  waveguide",  J. Plasma Phys., (1990), 43, 51.

  62.  Ivanov S.T., Alexov E.G., "Cyclotron waves in a plasma-filled waveguide",  Sov. J. Plasma Phys. (USA), 1989, 15, 657.

  63.  Ivanov S.T, Alexov E.G., "Electromagnetic waves in waveguide partially filled with semiconductor plasma", Contrib. Plasma Phys., (1990), 30, 763.

  64.  Ivanov S.T., Alexov E.G., Malinov P.N., "Nonsymmetrical electromagnetic waves in partially plasma - filled waveguide", Contrib. Plasma Phys., (1990), 30, 755.

  65.  Ivanov S.T., Alexov E.G., "Electromagnetic waves in the semiconductor plasma waveguide", Phys. Scripta, (1989),40, 58.

  66.  Ivanov S.T., Alexov E.G., Malinov P.N., "Symmetrical electromagnetic waves in partially-filled plasma waveguide", Plasma Phys. Control. Fusion, (1989), 31, 941.

  67.  Alexov E.G., Ivanov S.T. , "Electromagnetic waves in plasma waveguide", Sov. J. Plasma Phys. (USA), (1988), 14, 883.

 

 

For contact information, please, see Alexov webpage  at Clemson University

 

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