... Luthey-Schulten ¹

P. O'Donoghue and Z. Luthey-Schulten. ``Evolution of Structure in Aminoacyl-tRNA Synthetases'' MMBR, 67(4):550-73. December, 2003.

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... included ²

R.B. Russell and G.J. Barton. ``Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.'' Proteins: Struct. Func. Genet., 14:309-323. 1992.

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... sequence³

FASTA files.

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... structure⁴

The ASTRAL database (http://astral.stanford.edu) is a compendium of protein domain structures derived from the PDB database. It divides each protein structure into its domain components. For example, AspRS is divided into three separate PDB files: one containing the catalytic domain, one with the insertion domain, and one for the anticodon binding domain. The names of the files contain the PDB extension, the letter a for ASTRAL, and a number, which corresponds to which domain it is in the original PDB file. The PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids.

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... Structure⁵

See VMD Manual for supported formats

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...fig:select_nr).⁶

For more information about QR, see: Anurag Sethi, Patrick O'Donoghue, and Zaida Luthey-Schulten. ``Evolutionary profiles from the QR factorization of multiple sequence alignments" PNAS, 102(11):4045-4055. March, 2005.

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... RGB⁷

For more information about coloring methods, please refer to the VMD manual.

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... VMD⁸

For more information about drawing methods, please refer to the VMD manual.

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... Display⁹

For more information about coloring methods, please refer to the VMD manual.

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