Computational protocol: Over-Expression of 60s Ribosomal L23a Is Associated with Cellular Proliferation in SAG Resistant Clinical Isolates of Leishmania donovani

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Protocol publication

[…] Amino acid sequence of L. donovani 60sRL23a (Uniprot id: D1M863) was used for homology modeling. The Hidden Markov model based profile-profile alignment algorithm available at HHpred server on the bioinformatics toolkit platform of the Max Planck Institute for Developmental Biology (http://toolkit.tuebingen.mpg.de/hhpred) was used to find best template in PDB database for homology modeling with default settings . HHpred uses HMM based profile-profile alignment method for identification and alignment of homologous protein. After ensuring high degree of accuracy in alignment, ten homology models were built using Modeller 9.10 with thorough optimization . Final model was selected on the basis of DOPE score and structural validations were performed by using SAVS server. (http://nihserver.mbi.ucla.edu/SAVES_3/). […]

Pipeline specifications

Software tools HHPred, MODELLER
Application Protein structure analysis
Organisms Leishmania donovani, Escherichia coli, Mus musculus
Diseases Parasitic Diseases