Minimizing and Learning Energy Functions for Side-Chain Prediction
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[1] R. Goldstein. Efficient rotamer elimination applied to protein side-chains and related spin glasses. , 1994, Biophysical journal.
[2] Johan Desmet,et al. The dead-end elimination theorem and its use in protein side-chain positioning , 1992, Nature.
[3] M. Karplus,et al. Effective energy function for proteins in solution , 1999, Proteins.
[4] Jack Snoeyink,et al. An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem , 2004, Pacific Symposium on Biocomputing.
[5] D. Baker,et al. Modeling structurally variable regions in homologous proteins with rosetta , 2004, Proteins.
[6] Mark W. Schmidt,et al. Accelerated training of conditional random fields with stochastic gradient methods , 2006, ICML.
[7] Mona Singh,et al. Solving and analyzing side-chain positioning problems using linear and integer programming , 2005, Bioinform..
[8] Roland L. Dunbrack,et al. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.
[9] Martin J. Wainwright,et al. MAP estimation via agreement on trees: message-passing and linear programming , 2005, IEEE Transactions on Information Theory.
[10] O. Schueler‐Furman,et al. Improved side‐chain modeling for protein–protein docking , 2005, Protein science : a publication of the Protein Society.
[11] Adrian A Canutescu,et al. A graph‐theory algorithm for rapid protein side‐chain prediction , 2003, Protein science : a publication of the Protein Society.
[12] D. Baker,et al. Native protein sequences are close to optimal for their structures. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[13] Xiaojin Zhu,et al. Kernel conditional random fields: representation and clique selection , 2004, ICML.
[14] Jeffrey J. Gray,et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.
[15] Yi Liu,et al. RosettaDesign server for protein design , 2006, Nucleic Acids Res..
[16] S. L. Mayo,et al. Conformational splitting: A more powerful criterion for dead‐end elimination , 2000 .
[17] D. Baker,et al. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. , 2003, Journal of molecular biology.
[18] A Joshua Wand,et al. Improved side‐chain prediction accuracy using an ab initio potential energy function and a very large rotamer library , 2004, Protein science : a publication of the Protein Society.
[19] D. Baker,et al. High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design , 2007, Journal of molecular biology.