References

Citations and related literature

Thereotical and related literature

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Biopython citation

  1. Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423

  2. Chapman BA and Chang JT (2000). Biopython: Python tools for computational biology. ACM SIGBIO Newsletter, 20, 15-19

  3. Hamelryck T and Manderick B (2003) PDB file parser and structure class implemented in Python. Bioinformatics, 22, 2308-2310

  4. de Hoon MJ, Imoto S, Nolan J and Miyano S (2004) Open source clustering software. Bioinformatics, 20, 1454-1453

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  6. Cock PJ, Fields CJ, Goto N, Heuer ML and Rice PM (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res., 38, 1767-1771

  7. Talevich E, Invergo BM, Cock PJ and Chapman BA (2012) Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics, 13, 209

Modeller citation

  1. B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics 54, John Wiley & Sons, Inc., 5.6.1-5.6.37, 2016.

  2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.

  3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

  4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.

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