摘要: Side-chain prediction is an important subtask in the protein-folding problem. We show that finding a minimal energy side-chain con (cid: 173) figuration is equivalent to performing …
nips.cc参考文章(14)
Yair Weiss, Kevin P. Murphy, Michael I. Jordan, Loopy belief propagation for approximate inference: an empirical study uncertainty in artificial intelligence. pp. 467- 475 ,(1999)
Johan Desmet, Marc De Maeyer, Bart Hazes, Ignace Lasters, THE DEAD-END ELIMINATION THEOREM AND ITS USE IN PROTEIN SIDE-CHAIN POSITIONING Nature. ,vol. 356, pp. 539- 542 ,(1992) , 10.1038/356539A0
Jonathan S. Yedidia, Yair Weiss, William T. Freeman, Understanding belief propagation and its generalizations Exploring artificial intelligence in the new millennium. pp. 239- 269 ,(2003)
Roland L. Dunbrack, Martin Karplus, Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction Journal of Molecular Biology. ,vol. 230, pp. 543- 574 ,(1993) , 10.1006/JMBI.1993.1170
Zhexin Xiang, Barry Honig, Extending the accuracy limits of prediction for side-chain conformations. Journal of Molecular Biology. ,vol. 311, pp. 421- 430 ,(2001) , 10.1006/JMBI.2001.4865
Joaquim Mendes, Cl�udio M. Soares, Maria Arm�nia Carrondo, Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. Biopolymers. ,vol. 50, pp. 111- 131 ,(1999) , 10.1002/(SICI)1097-0282(199908)50:2<111::AID-BIP1>3.0.CO;2-N
Loren L. Looger, Homme W. Hellinga, Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics Journal of Molecular Biology. ,vol. 307, pp. 429- 445 ,(2001) , 10.1006/JMBI.2000.4424
Y. Weiss, W.T. Freeman, On the optimality of solutions of the max-product belief-propagation algorithm in arbitrary graphs IEEE Transactions on Information Theory. ,vol. 47, pp. 736- 744 ,(2001) , 10.1109/18.910585
Enoch S. Huang, Patrice Koehl, Michael Levitt, Rohit V. Pappu, Jay W. Ponder, Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods Proteins: Structure, Function, and Genetics. ,vol. 33, pp. 204- 217 ,(1998) , 10.1002/(SICI)1097-0134(19981101)33:2<204::AID-PROT5>3.0.CO;2-I
Brendan J. Frey, Ralf Koetter, Nemanja Petrovic, Very loopy belief propagation for unwrapping phase images neural information processing systems. pp. 737- 743 ,(2001)