Computational protocol: Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model

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Protocol publication

[…] In vitro aggregation and secondary structure prediction were accomplished by using the TANGO software . Tango calculates the partition function of the conformational phase space assuming that every segment on the protein populates one state: random coil, β-turn, α-helix, α-helix aggregation and β-sheet aggregation. Therefore, TANGO software can predict aggregation in solution, taking into account only structural parameters determined by the peptide sequence.In vivo aggregation was computed using AGGRESCAN, an algorithm based on an amino acid aggregation-propensity scale derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. The algorithm can actually predict the aggregation propensity of peptides in the presence of cell material .The isoelectric point (pI) was computed using the Expasy reference values and the peptide hydrophobic mean character using the GRAVY scale (http://expasy.org).To study the differences in these parameters between AMPs and non-AMPs a two-tailed unpaired t-test analysis with a confidence interval of 95% has been used. All the parameters computed are considered to be independent as a correlation lower than 0.9 is observed between them in all the databases described above. […]

Pipeline specifications

Software tools TANGO, AGGRESCAN
Databases ExPASy
Application Protein physicochemical analysis
Diseases Bacterial Infections, Blood Platelet Disorders, Drug-Related Side Effects and Adverse Reactions
Chemicals Adenosine Monophosphate