Jeffery G. Saven

 
 
Department of Chemistry
 
   
 
 

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  1. J. G. Saven, Computational protein design: advances in the design and redesign of biomolecular nanostructures. Current Opinion in Colloid & Interface Science, 2009. [doi]

  2. Mark E. Peterson, Feng Chen, Jeffery G. Saven, David S. Roos, Patricia C. Babbitt, and Andrej Sali. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Science, 2009. 18:1306 - 1315. [doi]

  3. J. Tang, S.-G. Kang, J. G. Saven and F. Gai. Characterization of Cofactor-Induced Folding Mechanism of a Zinc Binding Peptide Using Computationally Designed Mutants. Journal of Molecular Biology, 2009. 389: 90-102. [doi]

  4. Youn K. Kang, One-Sun Lee, Pravas Deria, Sang Hoon Kim, Tae-Hong Park, Dawn A. Bonnell, Jeffery G. Saven and Michael J. Therien. Helical Wrapping of Single-Walled Carbon Nanotubes by Water Soluble, Rigid Rod-like Poly(p-phenyleneethynylene). Nano Letters, 2009. 9: 1414–1418. [doi]

  5. S. Szep, S. Park, E Boder, G. Van Duyne, J. G. Saven. An interior water is essential for maintaining the structure of FKBP12. Proteins: Structure, Function, Bioinformatics, 2009. 74: 603-611. [doi]

  6. C. A. Butts, J. Swift, S.-G. Kang, L. Di Costanzo, D. W. Christianson, J. G. Saven, and I. J. Dmochowski. Directing Noble Metal Ion Chemistry within a Designed Ferritin Protein. Biochemistry, 2008. 47: 12729–12739. [doi]

  7. McAllister, Karen; Zou, Hongling; Cochran, Frank; Bender, Gretchen; Senes, Alessandro; Fry, H.; Nanda, Vikas; Keenan, Patricia; Lear, James; Saven, Jeffery; Therien, Michael; Blasie, J. Kent; DeGrado, William. Using alpha-Helical Coiled-Coils to Design Nanostructured Metalloporphyrin Arrays. Journal of the American Chemical Society, 2008. 130: 11921-11927. [doi]

  8. Pascal Philibert, Audrey Stoessel, Wei Wang, Annie-Paule Sibler, Jeffery G. Saven, Jérôme Courtête, Etienne Weiss and Pierre Martineau, Construction of a large focused antibody library for intrabody selection. BMC Biotechnology, 2007. 7: 81(article number).[doi]

  9. Gretchen M. Bender, Andreas Lehmann, Hongling Zou, Hong Cheng, H. Christopher Fry, Don Engel, Michael J. Therien, J. Kent Blasie, Heinrich Roder, Jeffrey G. Saven, and William F. DeGrado, De Novo Design of a Single Chain Diphenylporphyrin Metalloprotein. Journal of the American Chemical Society, 2007. 129: 10732-10740.[doi]

  10. Seung-Gu Kang and Jeffery G. Saven, Computational protein design: structure, function and combinatorial diversity. Current Opinion in Chemical Biology, 2007. 11: 329-334. [doi]

  11. Pramit, Chowdhury, Wei Wang, Michelle R Bunagan, Jason W. Klemke, Jia Tang, Stacey Lavender, Jeffrey G. Saven, Barry S. Cooperman, Feng Gai, Fluorescence correlation spectroscopy study of serpin depolymerization by computationally designed peptides. Journal of Molecular Biology, 2007. 369:462-473.[doi]

  12. B. North, L. Cristian, X. Fu Stowell, J. D. Lear, J. G. Saven, W. F. DeGrado, Characterization of a Membrane Protein Folding Motif, the Ser Zipper, Using Designed Peptides. Journal of Molecular Biology, 2006. 359: 930-939.[doi]

  13. J. Swift, W. A. Wehbi, B. D. Kelly, X. Fu Stowell, J. G. Saven, and I. J. Dmochowski, Design of Functional Ferritin-like Proteins with Hydrophobic Cavities. The Journal of the American Chemical Society, 2006. 128: 6611-6619.[doi]

  14. S. Park, Y. Xu, X. Fu Stowell, F. Gai, J. G. Saven and E. T. Boder, Limitations of yeast surface display in engineering proteins of high thermostability. Protein Engineering Design & Selection, 2006. 19: 211 – 217.[doi]

  15. J. Bronson, O.-S. Lee and J. G. Saven, Molecular dynamics simulation of a water soluble analog of the potassium channel KcsA. Biophysical Journal, 2006. 90: 1156-1163.[doi]

  16. S. Park and J. G. Saven. Simulation of pH-dependent edge strand rearrangement in human beta-2 microglobulin. Protein Science. 2006. 15: 200-207.[doi]

  17. M. R. Bunagan, X. Yang, J. G. Saven and F. Gai, Ultrafast Folding of a Computationally Designed Trp-cage Mutant: Trp2-cage. The Journal of Physical Chemistry B. 2006. 110: 3759-3763.[doi]

  18. H. Kono, W. Wang, and J. G. Saven, Combinatorial design strategies. Protein Engineering Protocols (eds., K. Müller, K. Arndt) published as part of the series Methods in Molecular Biology, v. 352 (Humana Press), 2006, pp. 3-22.

  19. P. Biswas, J. Zou, and J. G. Saven, Statistical theory for protein ensembles with designed energy landscapes. Journal of Chemical Physics, 2005. 123: 154908 (12 pages).[doi]

  20. S. Park and J. G. Saven, Statistical and molecular dynamics studies of buriedwater molecules in proteins. PROTEINS, Structure, Function, and Bioinformatics, 2005. 60: 450-463.[doi]

  21. S. Park, E. T. Boder, and J. G. Saven, Modulating the DNA affinity of Elk-1 with computationally selected mutations. The Journal of Molecular Biology, 2005. 348: 75-83. [doi]

  22. V. Nanda, M.l M. Rosenblatt, A. Osyczka, H. Kono, Z. Getahun, P. L. Dutton, J. G. Saven, W. F. DeGrado, De Novo Design of a Redox Active Minimal Rubredoxin Mimic. Journal of the American Chemical Society, 2005. 127: 5804-5805. [doi]

  23. F. V. Cochran, S. P. Wu, W. Wang, V. Nanda, J. G. Saven, M. J. Therien, W. F. DeGrado, Computational de novo design and characterization of a four-helix bundle protein that selectively binds a non-biological cofactor. Journal of the American Chemical Society, 2005. 127: 1346 - 1347.[doi]

  24. X. Yang and J. G. Saven, Computational methods for protein design and protein sequence variability: biased Monte Carlo and replica exchange, Chemical Physics Letters, 2005. 401: 205-210. [doi]

  25. S. Park and J. G. Saven, Computationally assisted protein design. Annual Reports in Computational Chemistry, 2005. 1: 245-253. [preprint, Elsevier site]

  26. S. Park, H. Kono, W. Wang, E. T. Boder, and J. G. Saven, Progress in the development and application of computational methods for probabilistic protein design. Computers and Chemical Engineering, 2005. 29:407-421.[doi]

  27. S. Park, X. Yang, and J. G. Saven, Advances in computational protein design, Current Opinions in Structural Biology, 2004. 14: 487-494 [doi]

  28. O.-S. Lee and J. G. Saven, Simulation studies of a helical m-phenylene ethynylene foldamer. Journal of Physical Chemistry B, 2004. 108: 11988-11994. [doi]

  29. Y. Zhu, X. Fu, T. Wang, A. Tamura, S. Takada, J. G. Saven, and F. Gai, Guiding the search for a protein’s maximum rate of folding, Chemical Physics, 2004. 307: 99-109.[doi]

  30. A. M. Slovic, H. Kono, J. D. Lear, J. G. Saven, and W. F. DeGrado, Computational design of water soluble analogues of the potassium channel KcsA. Proc. Natl. Acad. Sci. USA, 2004. 101: 1828-1833.[doi]

  31. X. Fu, H. Kono, and J. G. Saven, Probabilistic Approach to the Design of Symmetric
    Protein Quaternary Structures. Protein Engineering, 2003. 16: 971-977.[journal]

  32. J. R. Calhoun, H. Kono, S. Lahr, W. Wang, and W. F. DeGrado, and J. G. Saven. Computational design and characterization of a monomeric helical dinuclear metalloprotein. The Journal of Molecular Biology, 2003. 334: 1101-1115. [doi]

  33. H. Kono and J. G. Saven, Combinatorial protein design. Journal of Biophysics (Japan), 2003. 43: 186-191.

  34. J. G. Saven, Connecting statistical and optimized potentials for protein folding via a generalized foldability criterion, The Journal of Chemical Physics, 2003. 118: 6133-6136. [doi]

  35. J. Zou and J. G. Saven, Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences, The Journal of Chemical Physics, 2003. 118: 3843–3854.[doi]

  36. W. Wang and J. G. Saven, Designing gene libraries from protein profiles for combinatorial protein experiments, Nucleic Acids Research, 2002. 30: e120.[doi]

  37. J. G. Saven, Combinatorial protein design. Current Opinion in Structural Biology, 2002. 12: 453-458. [doi]

  38. J. G. Saven, Designing protein energy landscapes.Chemical Reviews, 2001. 101: 3113-3130.[doi]

  39. H. Kono and J. G. Saven, Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main chain structure. The Journal of Molecular Biology, 2001. 306: 607-627.[doi]

  40. J. Zou and J. G. Saven, Statistical Theory of Combinatorial Libraries of Proteins. Energetic Discrimination of a Target Structure. The Journal of Molecular Biology, 2000. 296: 281-294.[doi]

  41. R. B. Prince, J. G. Saven, P. G. Wolynes and J. S. Moore, The Cooperative Conformational Transition in Phenylene Ethynylene Oligomers: Chain-Length Dependence. The Journal of the Americal Chemical Society, 1999. 121: 3114-3121. [doi]

  42. J. C. Nelson, J. G. Saven, J. S. Moore and P. G. Wolynes, Solvophobically Driven Folding of Nonbiological Oligomers. Science, 1997. 277: 1793-1796.

  43. J. G. Saven and P. G. Wolynes, Statistical Mechanics of the Combinatorial Synthesis and Analysis of Folding Macromolecules. The Journal of Physical Chemistry B, 1997. 101: 8375-8389. [doi]

  44. J. G. Saven and P. G. Wolynes, Local Signals and the Energy Landscape of Collapsed, Helical Proteins. Physica D, 1997. 107: 330-337.

  45. M. D. Stephens, J. G. Saven and J. L. Skinner, Molecular Theory of Electronic Spectroscopy in Nonpolar Fludis: Ultrafast Solvation Dynamics and Absorption and Emission Line Shapes. The Journal of Chemical Physics, 1997. 106: 2129-2144. [doi]

  46. J. G. Saven and P. G. Wolynes, Local Conformational Signals and the Statistical Thermodynamics of Collapsed Helical Proteins. The Journal of Molecular Biology, 1996. 257: 199-216. [doi]

  47. J. Wang, J. G. Saven and P. G. Wolynes, Kinetics in Globally Connected, Correlated Random Energy Model. The Journal of Chemical Physics, 1996. 105: 11276-11284.[doi]

  48. J. G. Saven, J. Wang and P. G. Wolynes, Kinetics of Protein Folding: The Dynamics of Globally Connected Rough Energy Landscapes with Biases. The Journal of Chemical Physics, 1994. 101: 11037-11043.[doi]

  49. J. G. Saven and J. G. Skinner, A Molecular Theory of the Line Shape: Inhomogeneous and Homogeneous Electronic Spectra of Dilute Chromophores in Nonpolar Fluids. The Journal of Chemical Physics, 1993. 99: 4391-4402.[doi]

  50. J. G. Saven, J. L. Skinner and J. R. Wright, Classical and Quantum Continuum Percolation with Hard Core Interactions. The Journal of Chemical Physics, 1991. 94: 6153-6159. [doi]