On the algorithmic implementation of multiclass kernel-based vector machines
The Journal of Machine Learning Research
Support vector machine learning for interdependent and structured output spaces
ICML '04 Proceedings of the twenty-first international conference on Machine learning
Large Margin Methods for Structured and Interdependent Output Variables
The Journal of Machine Learning Research
Fast and accurate algorithms for protein side-chain packing
Journal of the ACM (JACM)
Nearest-Neighbor Methods in Learning and Vision: Theory and Practice (Neural Information Processing)
Nearest-Neighbor Methods in Learning and Vision: Theory and Practice (Neural Information Processing)
A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies
INFORMS Journal on Computing
Minimizing and learning energy functions for side-chain prediction
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Rapid protein side-chain packing via tree decomposition
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
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High-accuracy protein structure modeling demands accurate and very fast side chain prediction since such a procedure must be repeatedly called at each step of structure refinement. Many known side chain prediction programs, such as SCWRL and TreePack, depend on the philosophy that global information and pairwise energy function must be used to achieve high accuracy. These programs are too slow to be used in the case when side chain packing has to be used thousands of times, such as protein structure refinement and protein design. We present an unexpected study that local backbone information can determine side chain conformations accurately. LocalPack, our side chain packing program which is based on only local information, achieves equal accuracy as SCWRL and TreePack, yet runs 4-14 times faster, hence providing a key missing piece in our efforts to high-accuracy protein structure modeling.