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Title
Trends in template/fragment-free protein structure prediction
Authors
Keywords
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Journal
THEORETICAL CHEMISTRY ACCOUNTS
Volume 128, Issue 1, Pages 3-16
Publisher
Springer Nature
Online
2010-08-31
DOI
10.1007/s00214-010-0799-2
References
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Note: Only part of the references are listed.- Fragment-free approach to protein folding using conditional neural fields
- (2010) F. Zhao et al. BIOINFORMATICS
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- Lessons from Structural Genomics
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- Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction
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