• Holm L, Sander C. 1992. Evaluation of protein models by atomic solvation preference. J Mol Biol 225: 93105.
  • Huang E, Subbiah S, Tsai J, Levitt M. 1996. Using a hydrophobic contact potential to evaluate native and near–native folds generated by molecular dynamics simulations. J Mol Biol 257: 716725.
  • Lazaridis T, Karplus M. 1999. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 288: 477487.
  • Novotny J, Bruccoleri R, Karplus M. 1984. An analysis of incorrectly folded protein models. Implications for structure predictions. J Mol Biol 177: 787818.
  • Park B, Huang E, Levitt M. 1997. Factors affecting the ability of energy func–tions to discriminate correct from incorrect folds. J Mol Biol 266: 831846.
  • Park B, Levitt M. 1996. Energy functions that discriminate X–ray and near native folds from well–constructed decoys. J Mol Biol 258: 367392.
  • Samudrala R, Moult J. 1998. An all–atom distance dependent conditional prob–ability discriminatory function for protein structure prediction. J Mol Biol 275: 895916.
  • Samudrala R, Xia Y, Huang E, Levitt M. 1999. Ab initio protein structure prediction using a combined hierarchical approach. Proteins Struct Funct Genet S 3: 194198.
  • Samudrala R, Xia Y, Levitt M, Cotton N, Huang E, Davis R. 2000. Probing structure–function relationships of the dna polymerase alpha–associated zinc–finger protein using computational approaches. In: AltmanR, DunkerA, HunterL, KleinT, LauderdaleK, eds. Proceedings of the Pacific Symposium on Biocomputing. Singapore: World Scientific Press. pp 179189.
  • Simons K, Bonneau R, Ruczinski I, Baker D. 1999a. Ab initio structure pre–diction of CASP3 targets using ROSETTA. Proteins Struct Funct Genet S 3: 171176.
  • Simons K, Ruczinski I, Kooperberg C, Fox B, Bystroff C, Baker D. 1999b. Improved recognition of native–like protein structures using a combination of sequence–dependent and sequence–independent features of proteins. Proteins Struct Funct Genet 34: 8295.
  • Subramaniam S, Tcheng DK, Fenton J. 1996. A knowledge–based method for protein structure refinement and prediction. In: StatesD, AgarwalP, Gaas–terlandT, HunterL, SmithR, eds. Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology. Menlo Park, California: AAAI Press. pp 218229.
  • Wang Y, Zhang H, Scott R. 1995. Discriminating compact non–native structures from the native structure of globular proteins. Proc Natl Acad Sci USA 92: 709713.
  • Wei L, Huang E, Altman R. 1999. Are predicted structures good enough to preserve functional sites. Structure 7: 643650.