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Simons, K.T.; Ruczinski, I.; Kooperberg, C.; Fox, B.A.; Bystroff, C.; Baker, D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999, 34, 82 -- 95.

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On Design of Optimal Nonlinear Kernel Potential Function for.. - Hu, Li, Liang (2003)   (Correct)

....[5 8] In this class of potentials, the interaction between a pair of residues are estimated from its relative frequency in database when compared with a reference state or a null model. This approach has been successfully applied in fold recognition, in threading, and in many other studies [7 14]. The drawback of this class of potential is that there are several conceptual di#culties. These include the neglect of chain connectivity in the reference state, and the problematic implicit assumption of Boltzmann distribution [15 17] An alternative approach is to find a set of parameters such ....

Simons KT, Ruczinski I, Kooperberg C, Fox B, Bystro# C, Baker D. Improved recognition of nativelike protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82--95.


Protein Sequence Optimization - Theory, Practice, and Fundamental.. - Torda (2004)   (Correct)

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Simons, K.T.; Ruczinski, I.; Kooperberg, C.; Fox, B.A.; Bystroff, C.; Baker, D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999, 34, 82 -- 95.


Genome Informatics 14: 228--237 (2003) Development of an.. - Prediction System Able   (Correct)

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Simons, K.T., Ruczinski, I., Kooperberg, C., Fox, B.A., Bystro#, C., and Baker, D., Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins, Proteins, 34:82--95, 1999.


Effective Energy Functions for Protein Structure Prediction - Lazaridis, Karplus   (Correct)

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Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D: Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999, 34:82-95.


Rosetta in CASP4: Progress in Ab Initio Protein.. - Bonneau, Tsai.. (2001)   (3 citations)  (Correct)

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Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82--95.


Improving the Performance of Rosetta Using Multiple.. - Bonneau, Strauss, Baker (2001)   (Correct)

No context found.

Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82--95.

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