J. M. Sauder, J. W. Arthur, and R. L. Dunbrack Jr. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins: Structure, Function, and Genetics, 40(1):6-- 22, 2000. Home/Search Document Details and Download
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Genomic Fold Assignment and Rational Modeling of Proteins.. - Sauder, Dunbrack, Jr. Self-citation (Sauder Dunbrack) (Correct)
....have performed a rigorous analysis of the accuracy of the alignments generated by BLAST PSI BLAST. Since the quality of an alignment is the single most important factor in homology modeling, we also assessed the alignment accuracy of BLAST and PSI BLAST as a precursor to genomic fold assignment (Sauder et al. 2000). However, a protein structure model based on a homologous PDB structure is of little or no value unless there is a context for its use and interpretation. The utility of a model is generally correlated to the amount of experimental data that is available for the protein and or how much is ....
.... PSI BLAST generates fairly accurate and long alignments, in contrast to global alignment programs such as CLUSTALW, where the alignments have more errors below 30 sequence identity, and pairwise local alignment programs such as BLAST, where the alignments are accurate but prematurely truncated (Sauder et al. 2000). These two situations are illustrated in Figure 1, where the results from the most difficult superfamily level comparisons are shown. A total of 30,000 superfamily level alignments were performed, where 99 of the sequences share less than 30 identity. The top panel reports the fraction correct ....
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Sauder, J. M., Arthur, J. W. and Dunbrack, R. L., Jr. 2000. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 40:6-22.
Progress: : Simultaneous Searching Of Protein . . . - Bhattacharya, al. (Correct)
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J. M. Sauder, J. W. Arthur, and R. L. Dunbrack Jr. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins: Structure, Function, and Genetics, 40(1):6-- 22, 2000.
ProGreSS: SIMULTANEOUS SEARCHING OF PROTEIN.. - Bhattacharya.. (2004) (1 citation) (Correct)
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J. M. Sauder, J. W. Arthur, and R. L. Dunbrack Jr. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins: Structure, Function, and Genetics, 40(1):6--22, 2000.
Benchmarking tools for the alignment of functional.. - Casey Bergman Cbergman (2004) (Correct)
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Sauder JM, Arthur JW, Dunbrack RL, Jr.: Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 2000, 40:6-22.
A database and tools for 3-D protein structure comparison.. - Shindyalov, Bourne (2001) (Correct)
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Sauder,J.M., Arthur,J.W. and Dunbrack,R.L.,Jr (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins, 40, 6--22.
Including Biological Literature Improves Homology Search - Chang, Raychaudhuri, Altman (2001) (1 citation) (Correct)
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Sauder, J. M., Arthur, J. W. and Dunbrack Jr, R. L. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 40, 6-22 (2000).
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