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Introduction
Method and Applications
Method
Applications
References
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Bower MJ, Cohen FE, Dunbrack RL (1997) Prediction of protein side chain rotamers from a backbone dependent rotamer library: a new homology modeling tool. J Mol Biol 267:1268–1282
Bruccoleri RE, Karplus M (1987) Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolym 26:137–168
de Bakker PIW, DePristo MA, Burke DF, Blundell TL (2003) Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized Born solvation model. Proteins: Struct Funct Bioinform 51:21–40
DePristo MA, de Bakker PIW, Lovell SC, Blundell TL (2003) Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles. Proteins: Struct Funct Bioinform 51:41–55
Fiser A, Do RKG, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753–1773
Gill PE, Murray W, Saunders MA, Wright MH (1986) NPSOL 4.0 User's Guide. Systems Optimization Laboratory, Dept. of Operations Research, Stanford University, CA
Hartigan JA, Wong MA (1979) Algorithm AS 136: A K-means clustering algorithm. Appl Stat 28:100–108
Jacobson MP, Pincus DL, Rappa CS, Day TJF, Honig B, Shaw DE, Friesner RA (2004) A hierarchical approach to all-atom protein loop prediction. Proteins: Struct Funct Bioinform 55:351–367
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features. Biopolym 22:2577–2637
Klepeis JL, Floudas CA (1999) Free energy calculations for peptides via deterministic global optimization. J Chem Phys 110:7491–7512
Klepeis JL, Floudas CA (2002) Ab initio prediction of helical segments in polypeptides. J Comput Chem 23:245–266
Klepeis JL, Floudas CA (2003) Ab initio tertiary structure prediction of proteins. J Glob Optim 25:113–140
Klepeis JL, Floudas CA (2003) ASTRO-FOLD: A combinatorial and global optimization framework for ab initio prediction of three‐dimensional structures of proteins from the amino acid sequence. Biophys J 85:2119–2146
Klepeis J, Floudas C (2003) Prediction of beta-sheet topology and disulfide bridges in polypeptides. J Comput Chem 24(2):191–208
Klepeis JL, Floudas CA (2005) Analysis and prediction of loop segments in protein structure. Comput Chem Eng 29(3):423–436
Klepeis JL, Floudas CA, Morikis D, Lambris JD (1999) Predicting peptide structures using nmr data and deterministic global optimization. J Comput Chem 20:1354–1370
Klepeis JL, Pieja MT, Floudas CA (2003) A new class of hybrid global optimization algorithms for peptide structure prediction: Integrated hybrids. Comput Phys Commun 151:121–140
Klepeis JL, Pieja MT, Floudas CA (2003) Hybrid global optimization algorithms for protein structure prediction: Alternating hybrids. Biophys J 84:869–882
Klepeis J, Wei Y, Hecht M, Floudas C (2005) Ab initio prediction of the 3‑dimensional structure of a de novo designed protein: A double blind case study. Proteins: Struct Funct Bioinform 58:560–570
Mönnigmann M, Floudas CA (2005) Protein loop structure prediction with flexible stem geometries. Proteins: Struct Funct Bioinform 61(4):748–762
Némethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA (1992) Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline‐containing peptides. J Phys Chem 96:6472–6484
Xiang Z, Soto C, Honig B (2002) Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proceedings of the National Academy of Sciences of the United States of America, vol 99. pp 7432–7437
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Mönnigmann, M., Floudas, C.A. (2008). Protein Loop Structure Prediction Methods . In: Floudas, C., Pardalos, P. (eds) Encyclopedia of Optimization. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-74759-0_530
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DOI: https://doi.org/10.1007/978-0-387-74759-0_530
Publisher Name: Springer, Boston, MA
Print ISBN: 978-0-387-74758-3
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