Computational protocol: Chlamydial Lipoproteins Stimulate Toll-Like Receptors 1/2 Mediated Inflammatory Responses through MyD88-Dependent Pathway

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Protocol publication

[…] The lipoprotein structures (D067, D381, D541, and D775) were initially built by homologous modeling using SWISS-MODEL (swissmodel.expasy.org). The initial models were then solvated in a water box and run 10,000 steps of energy minimization and 10 ns molecular dynamics using NAMD (NAnoscale Molecular Dynamics) v 2.9. The modeled lipoprotein-TLR complex structures were built by manually aligning the lipobox cysteine to the Pam3-cysteine based on the crystal structure of TLR2/TLR6- Pam2CSK4 complex (PDB code: 3A79). […]

Pipeline specifications

Software tools SWISS-MODEL, NAMD
Databases ExPASy
Application Protein structure analysis
Organisms Homo sapiens, Chlamydia trachomatis, Mus musculus
Chemicals Cysteine