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- Protein Science (1997), 6 6 7 M 8 8 . Cambridge University Press. Printedinthe USA. Copyright 0 1997 The Protein Society
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- J. Mol. Biol. (1997) 265, 217241 MONSSTER: A Method for Folding Globular Proteins
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- Biophysical Journal Volume 85 August 2003 11451164 1145 TOUCHSTONE II: A New Approach to Ab Initio Protein
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- J. Mol. Biol. (1995) 251, 448467 Prediction of Quaternary Structure of Coiled Coils.
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- Proc. Natl. Acad. Sci. USA Vol. 90, pp. 2099-2100, March 1993
- BioMed Central Page 1 of 10
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- Proc. Nat!. Acad. Sci. USA Vol. 85, pp. 5057-5061, July 1988
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