Computational protocol: Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles

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Protocol publication

[…] Pairwise sequence comparisons were carried out by Needleman and Wunsch alignment program of the EMBOSS package []. BLAST was used to perform local alignment []. BLOSUM62 scoring matrix and default values for gap penalties were used for sequence alignments. Multiple alignments and phylogenetic dendrograms were also constructed for each of the domain types using CLUSTALW program []. [...] For model building, the alignments with the template structure 1AMU were generated by program GenTHREADER []. The models of proteins were built by MODELLER 6V2[]. The model structures were optimized by conjugate gradient energy minimization and molecular dynamics with simulated annealing provided in the MODELLER program. The ligands for docking were built using the builder module of InsightII. The ligands were minimized before docking using the discover module of InsightII. […]

Pipeline specifications

Software tools EMBOSS, Clustal W, PSIPRED, MODELLER
Applications Phylogenetics, Protein structure analysis
Chemicals Acyl Coenzyme A, Coenzyme A