Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility

In comparative modeling, the quality of amino acid sequence alignment still constitutes a major bottleneck in the generation of high quality models of protein three‐dimensional (3D) structures. Substantial efforts have been made to improve alignment quality by revising the substitution matrix, intro...

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Veröffentlicht in:	Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2011-06, Vol.79 (6), p.1868-1877
Hauptverfasser:	Hijikata, Atsushi, Yura, Kei, Noguti, Tosiyuki, Go, Mitiko
Format:	Artikel
Sprache:	eng
Schlagworte:	ALAdeGAP amino acid sequence alignment Amino Acids - chemistry Bacillus subtilis Bacillus subtilis - chemistry Bacterial Proteins - chemistry comparative modeling Escherichia coli - chemistry Models, Molecular position dependent gap penalty Protein Conformation Sequence Alignment - methods solvent accessibility Solvents
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