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• W2072969046 abstract "The dead-end elimination (DEE) theorems are powerful tools for the combinatorial optimization of protein side-chain placement in protein design and homology modeling. In order to reach their full potential, the theorems must be extended to handle very hard problems. We present a suite of new algorithms within the DEE paradigm that significantly extend its range of convergence and reduce run time. As a demonstration, we show that a total protein design problem of 10(115) combinations, a hydrophobic core design problem of 10(244) combinations, and a side-chain placement problem of 10(1044) combinations are solved in less than two weeks, a day and a half, and an hour of CPU time, respectively. This extends the range of the method by approximately 53, 144 and 851 log-units, respectively, using modest computational resources. Small to average-sized protein domains can now be designed automatically, and side-chain placement calculations can be solved for nearly all sizes of proteins and protein complexes in the growing field of structural genomics." @default.
• W2072969046 created "2016-06-24" @default.
• W2072969046 creator A5054436322 @default.
• W2072969046 creator A5074445091 @default.
• W2072969046 date "2001-03-01" @default.
• W2072969046 modified "2023-09-25" @default.
• W2072969046 title "Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics" @default.
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• W2072969046 doi "https://doi.org/10.1006/jmbi.2000.4424" @default.
• W2072969046 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/11243829" @default.
• W2072969046 hasPublicationYear "2001" @default.
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