Computational protocol: Structure-Based Phylogeny as a Diagnostic for Functional Characterization of Proteins with a Cupin Fold

Similar protocols

Protocol publication

[…] DALI, a pairwise structural alignment algorithm , has been used for the alignment of protein domains with cupin fold. Simultaneous rigid-body structural superposition was performed using a robust multiple structural alignment algorithm MUSTANG . [...] Kitsch, a distance based algorithm from PHYLIP suite of programs was used for the generation of dendrograms . The dendrogram has been rendered using Dendroscope software . The individual domains of the proteins were considered for the phylogenetic analyses. An all against all pairwise comparison of these modules (domains) with cupin fold was performed using DALI algorithm. From the pairwise alignments, a distance matrix was computed in order to generate the dendrogram. A measure called structural distance metric (SDM), calculated as follows , was used to obtain the distance matrix. SDM can be defined as:where, w1 = (1-PFTE+1-SRMS)/2 and w2 = (PFTE+SRMS)/2 RMSD is the root mean square deviation in Å.The calculation of SDM includes parameters that account for indels as well as root mean square deviation at the topologically equivalent positions. The SDM values therefore provide a good measure to understand the extent of differences between the structures. […]

Pipeline specifications