I'm currently trying to get the 3D structure of a set of peptides (ranging from 12 to 20 aminoacids). Subsequently we want to make docking analysis against an enzyme.
Which software do you use for that? How do you refine the structure?
Thanks!
Such short peptides usually do not assume a single defined structure in solution. The structure of the peptide in the complex is not necessarily the dominant conformation in the ensemble of structures in solution, but induced by the interaction with the binding partner. As a consequence, rigid docking of peptides usually is not possible.
Article Peptide docking and structure-based characterization of pept...
https://arxiv.org/pdf/1505.01138.pdf
Chapter AnchorDock for Blind Flexible Docking of Peptides to Proteins
Article FlexPepDock lessons from CAPRI peptide-protein rounds and su...
Chapter Modeling Peptide-Protein Structure and Binding Using Monte C...
If you are sure about the structure of the peptide based on your wet lab experiments and binding with the receptor indicated by ITC studies/yeast two hybrid assay, or any other technique,
then you can use Biopolymer module of Sybyl X for generating the peptide structure. It has options for possible conformations of the peptide and also it minimizes the structure using either Tripos Force Field or any other force field given in the Sybyl suite.
Another method is to used robetta I-TASSER or any other web server for generating the structure.
As suggested by Annemarie, rigid docking is not feasible for peptides but you can use flexible docking approach by many softwares including HADDOCK, HEX, ZDOCK,etc.
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