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Publications

  • Nanda V, Zahid S, Xu F, Levine D. (2011) Computational design of intermolecular stability and specificity in protein self-assembly. Methods Enzymol. 487:575-93.

  • Nanda V, Koder RL. (2010) Designing artificial enzymes by intuition and computation. Nat Chem. Jan;2(1):15-24. Epub 2009 Dec 17. Review.

  • Braun P, Goldberg E, Negron C, von Jan M, Xu F, Nanda V, Koder RL, Noy D.(2011) Design principles for chlorophyll-binding sites in helical proteins. Proteins. Feb;79(2):463-76.

  • Xu F, Zhang L, Koder RL, Nanda V. (2010) De novo self-assembling collagen heterotrimers using explicit positive and negative design. Biochemistry. Mar 23;49(11):2307-16.

  • Annavarapu S, Nanda V. (2009) Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acids. BMC Struct Biol. 9:61.

  • Kar K, Ibrar S, Nanda V, Getz TM, Kunapuli SP, Brodsky B. (2009) Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures.
    Biochemistry. 48(33):7959-68.

  • Schmiedekamp A, Nanda V. (2009) Metal-activated histidine carbon donor hydrogen bonds contribute to metalloprotein folding and function. J Inorg Biochem. 103(7):1054-60.

  • Nanda V. Do-it-yourself Enzymes - News and Views (2008) Nature Chemical Biology, 4 , 273-275.
  • Nanda V, Xu F, Hsieh D. Chapter 18: Modulation of Intrinsic Protein Properties by Computational Design - Protein Engineering and Design (in press) CRC Press
  • McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. Using a-helical Coiled-Coils to Design Nanostructured Metalloporphyrin Arrays (2008) J. Am. Chem. Soc., 130, 11921-11927.
  • Nanda V, Schmiedekamp AM. Are Aromatic Carbon Donor Hydrogen Bonds Linear in Proteins? (2008) Proteins: SFB., 70, 489-497.
  • Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto C, Tereshko V, Nanda V, Stayrook S, DeGrado WF. Structural Basis for the Function and Inhibition of an Influenza Virus Proton Channel. (2008) Nature., 451, 596-599.
  • Senes A, Chadi DC, Law PB, Walters RFS, Nanda V, DeGrado WF. Ez, a Depth-dependent Potential for Assessing the Energies of Amino Acid Side-chains into Membranes: Derivation and Applications to Determining the Orientation of Transmembrane and Interfacial Helices. (2007) J. Mol. Biol., 366, 436-448.
  • Nanda V, Adrianarijaonna A, Narayanan C. The Role of Protein Homochirality in Shaping the Energy Landscape of Folding (2007) Prot. Sci., 16, 1667-1675.
  • Nanda V , DeGrado WF. Computational design of heterochiral peptides against a helical target. (2006) J. Am. Chem. Soc. 128 , 809-16.
  • Nanda V , Rosenblatt MM, Osyczka A, Kono H, Getahun Z, Dutton PL, Saven JG, DeGrado WF. De Novo Design of a Redox-Active Minimal Rubredoxin Mimic . (2005) J. Am. Chem. Soc. 127 , 5804-5.
  • Nanda V , DeGrado WF. Automated Use of Mutagenesis Data in Structure Prediction. (2005) Proteins: SFB . 59 , 454-66.
  • Adamian L, Nanda V , DeGrado WF, Liang J. Empirical Lipid Propensities of Amino Acid Residues in Multispan Helical Membrane Proteins. (2005) Proteins: SFB , 59 , 496-509.
  • Stouffer A, Nanda V , Lear JD, DeGrado WF. Sequence Determinants of a Membrane Proton Channel: An Inverse Relationship Between Stability and Function. (2005) J. Mol. Biol. 347 , 169-79.
  • Duong-Ly K, Nanda V , DeGrado WF, Howard KP. M2TM Tetramer Conformation Depends on Lipid Bilayer Environment. (2005) Prot. Sci . 14 , 856-61.
  • Cristian L, Nanda V , Lear JD, DeGrado WF. Synergistic Interactions between Aqueous and Membrane Domains of a Designed Protein Determine its Fold and Stability (2005) J. Mol Biol. 348 1225-33.
  • Nanda V , DeGrado WF. Simulated Evolution of Emergent Chiral Structures in Polyalanine. (2004) J. Am. Chem. Soc. 126 , 14459-67.