Abstract
This chapter describes the experimental results of the MRF-based method for homology detection and fold recognition including alignment accuracy, success rate, running time and contribution of some important features. This chapter also compares the MRF-based method with currently popular PSSM- and HMM-based methods such as HHpred, HHblits and FFAS, in terms of alignment accuracy and success rate of homology detection and fold recognition.
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References
Murzin, A.G.: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247(4), 536–540 (2013)
Andreeva, A.: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32(l), 226–229 (2004)
Andreeva, A.: Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 36(1), D419–D425 (2008)
Angermüller, C., Biegert, A., Söding, J.: Discriminative modelling of context-specific amino acid substitution probabilities. Bioinformatics 282(4), 3240–3247 (2012)
Eddy, S.R.: HMMER: Profile Hidden Markov Models for Biological Sequence Analysis (2001)
Söding, J.: Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7), 951–960 (2005)
Rychlewski, L.: Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 9(2), 232–241 (2000)
Remmert, M.: HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9(2), 173–175 (2012)
Zhang, Y., Skolnick, J.: TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33(7), 2302–2309 (2005)
Menke, M., Berger, B., Cowen, L.: Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol 4(1), e10 (2008)
Wang, S., et al.: Protein structure alignment beyond spatial proximity, vol. 3. Scientific Reports (2013)
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Xu, J., Wang, S., Ma, J. (2015). Experiments and Results. In: Protein Homology Detection Through Alignment of Markov Random Fields. SpringerBriefs in Computer Science. Springer, Cham. https://doi.org/10.1007/978-3-319-14914-1_4
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DOI: https://doi.org/10.1007/978-3-319-14914-1_4
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