R. Samudrala, Y. Xia, M. Levitt, and E.S. Huang. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein, and K. Lauderdale, editors, Proceedings of the Pacific Symposium on Biocomputing, pages 505--516, 1999. Home/Search Document Details and Download
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....RMSD around 2 A to the native structure. MJ and BT potential work better on 4rxn because they classify the four Cys Cys contacts as disulfide bonds. Lattice ssfit Set. The lattice ssfit set contains conformations for eight small proteins generated by ab initio protein structure prediction methods [44, 45]. The conformational space of a sequence was exhaustively enumerated on a tetrahedral lattice. A lattice based scoring function was used to select the 10,000 best scoring conformations. Secondary struc8 H# Hgc HMJ HBT Decoy set PDB Rank Z f 1, 000 Rank Z Rank Z Rank Z 4state 1ctf 1 ....
R. Samudrala, Y. Xia, M. Levitt, and E.S. Huang. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pac. Symp. Biocomput., 1999.
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R. Samudrala, Y. Xia, M. Levitt, and E.S. Huang. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein, and K. Lauderdale, editors, Proceedings of the Pacific Symposium on Biocomputing, pages 505--516, 1999.
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Samudrala,R., Xia,Y., Levitt,M. and Huang,E. (1999) A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In Altman,R., Dunker,A., Hunter,L., Klein,T. and Lauderdale,K. (eds), Proceedings of the Pacific Symposium on Biocomputing. World Scientific Press, pp. 505--516.
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.... consisted of copying torsion values for 3 residue fragments and the next few iterations would use torsion values from the 14 state model) The scoring function for minimisation is primarily a combination of the all atom function, a hydrophobic compactness function, and a bad contacts function [40]. The primary search technique we used was a Metropolis Monte Carlo (MC) procedure where conformations are accepted or rejected based on the Boltzmann s equation [41] Each trajectory was allowed 50,000 iterations, starting with a high temperature such that 99 of the moves were accepted for the ....
....were minimised using ENCAD [36] and scored using a combination of scoring functions that hierarchically reduces the total number of conformations produced to one final conformation. The scoring functions used for the final filtering include the all atom function [32] hydrophobic compactness [40], a simple residue residue contact function [44] a densityscoring function that is based on the distance of a conformation to all its relatives in the conformation pool, contact order [45] a secondary structure based scoring function that evaluates the match between the predicted structure and ....
Samudrala R, Xia Y, Levitt M, Huang E: A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In: Proceedings of the Pacific Symposium on Biocomputing (Edited by: Altman R, Dunker A, Hunter L, Klein T, Lauderdale K) World Scientific Press 1999, 505-516
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Samudrala R, Xia , Levitt M, Huang E. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In: Altman R, Dunker A, Hunter L, Klein T, Lauderdale, K, editors. Proceedings of the Pacific Symposium on Biocomputing. World Scientific Publishing Co: Singapore; 1999. p 505--516.
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R. Samudrala, Y. Xia, M. Levitt, and E.S. Huang. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein, and K. Lauderdale, editors, Proceedings of the Pacific Symposium on Biocomputing, pages 505--516, 1999.
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R. Samudrala, Y. Xia, M. Levitt, and E. Huang. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pac. Symp. Biocomput., 1999.
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Samudrala R, Xia Y, Levitt M, Huang ES. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pacific Symp Biocomput 1999;505--516.
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