Molecular sequence alignment

Zhang, C. and A. K. Wong, A genetic algorithm for multiple molecular sequence alignment. Comput Appl Biosci, 1997. 13(6) p. 565-81. 

Ortiz A R, A Kolinski and J Skolnick 1998. Fold Assembly of Small Proteins Using Monte C Simulations Driven by Restraints Derived from Multiple Sequence Alignments. Jourru Molecular Biology 277 419-446. 

A Apostolico, R Giancarlo. Sequence alignment in molecular biology. J Comput Biol 5 173-196, 1998. 

Due to the ready accessibility of SH2 domains by molecular biology techniques, numerous experimentally determined 3D structures of SH2 domains derived by X-ray crystallography as well as heteronuclear multidimensional NMR spectroscopy are known today. The current version of the protein structure database, accessible to the scientific community by, e.g., the Internet (http //www.rcsb.org/pdb/) contains around 80 entries of SH2 domain structures and complexes thereof. Today, the SH2 domain structures of Hck [62], Src [63-66], Abl [67], Grb2 [68-71], Syp [72], PLCy [73], Fyn [74], SAP [75], Lck [76,77], the C- and N-terminal SH2 domain ofp85a [78-80], and of the tandem SH2 domains Syk [81,82], ZAP70 [83,84], and SHP-2 [85] are determined. All SH2 domains display a conserved 3D structure as can be expected from multiple sequence alignments (Fig. 4). The common structural fold consists of a central three-stranded antiparallel ft sheet that is occasionally extended by one to three additional short strands (Fig. 5). This central ft sheet forms the spine of the domain which is flanked on both sides by regular a helices [49, 50,60]. 

Galtier, N., Gouy, M., and Gautier, C. (1996). SEAVIEW and PHYLO WIN two graphic tools for sequence alignment and molecular phylogeny. Comp. Appl. Biosci. 12, 543-548. 

Kumar, S., Tamura, K. and Nei, M. (2004) MEGA3 integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5, 150-163. 

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