Through the course of our project, we came across many avenues where there were tasks that could be optimized or were cumbersome due to limitations in tools or awareness. Identifying them and working to resolve these issues for further iGEMers has been a long-developed culture cultivated in all iGEM teams. Over our iGEM journey, we identified gaps that other teams might run into, thereby slowing their progress, and decided to address these gaps with the following.
Our software GRASP addresses the unavailability of reliable softwares that consider conformational changes while performing conserved mutations to a peptide sequence. Thus, GRASP is a unique tool that would help future iGEM teams perform conserved point mutations at respective sites. This software would help by simplifying the creation of appropriate conserved mutations to their corresponding sequence. Our software is one-of-a-kind in its approach to automating and exponentially simplifying the process of random conserved mutations, which allows the user to carry out protein/peptide engineering by virtue of forced evolution. GRASP, thus would enable users to design potential protein/peptide ligands for their protein of interest and even carry out rational interaction studies.
To know more about our software, visit our Software page.
The multitude of available tools to simulate Protein-Protein interactions and structure predictions, howsoever useful, comes with the added cost of not knowing which tool to use when and where. Our team faced the aforementioned issues when docking studies were carried out. Another iGEM team, IISER Pune 2 reported that they faced similar problems. This common ground of confusion inspired the handbook. It was made to ease the process of choosing a relevant tool from the array of available tools for upcoming iGEMers. In this handbook, we have compiled the algorithm and use cases of popular docking servers, along with an overview of Rigid and Flexible Docking while highlighting ClusPro and HADDOCK. We have also briefly gone over AlphaFold and ColabFold for the prediction of protein structures.
With our progress in the project, the Wet Lab team made a detailed itinerary of planned experiments. This curated handbook includes both experiments that were performed and perfected and ones that were just planned. The troubleshooting yielded the best possible results for each experiment, including plasmid isolation, competent cell preparation by CaCl2 method, PCR amplification etc. The primary objective of this handbook is to help other iGEM teams carry out these molecular biology experiments.
More information on our troubleshooting and experimentation timeline is available here.