 Dear students now as you know all the salient steps in homology modeling It's time to introduce a software that can help you to perform homology modeling in the In an automated way. Okay, so just to remind you of the salient steps that we looked at in homology modeling The first step in homology modeling included the template recognition That is the recognition or searching of sequences that are similar to the protein that you want to create the structure for secondly you align these sequences with the Query protein target protein and you optimize their alignment as well next You corrected the alignment in order for it to contain the minimum amounts of gaps and mismatches Next you created the backbone for the protein that you are going to create a structure for This will be followed by a loop modeling in which you will create all possible combinations of loops and then see which loops are most suitable to be placed onto the backbone in The next step you put the side chains That is the our groups that are attached to the amino acids onto the backbone So once you placed all the side chains then you have a backbone with all the our groups attached in a reasonable confirmation The model was optimized After this and validated using experimental data Now moving towards the software that can be used to perform all of these steps for you Of course, you would not want to do all of these steps yourself Manually because it will be very time-consuming and that since the protein sequence databases are very large You cannot possibly do it for 500,000 proteins So model is a tool that is available online by Sally lab and It is a commonly utilized tool It's a very powerful tool for homology modeling and you can use it if you know a little bit of Python programming language Which you can learn easily So the two inputs are the Python script that you will write and secondly the structure of the templates or the PDB Files for those proteins to begin with you have to write a Python script This will be the input to modeler and then It will be followed by the sequences for various proteins and Their alignments. So here is the ally file or the sequence alignment file Lastly you have to input the PDB for the template So here you go as you can see at a number one two three four alpha carbons their coordinates are given here So these are the three inputs that you provide to the Modular software. So what modeler does for you is for instance, if you have this template structure from the PDB and If you have let's say an amino acid side chain here valine Then it tries to substitute these amino acids by other amino acids such that the overall energy of the protein structure Becomes minimized. So as you can see in the yellow part valine has been substituted by Glutamine you can see the side chain is Different for valine and glutamine. So this is your initial model or INI file and Energy is minimized for the initial model by creating all the possible Rotomer configurations for glutamine in this case you can see the rotamer or the side chain has been rotated and therefore Lesser energy is now present in the structure and therefore the structure is more stable so this change in rotamer as Help you to minimize the energy and this is output as the output model So modeler can output several of these output models and you can select The best one from them according to the score Amongst the outputs so you have the dot log file which logs the output from the run the model generated in the PDB dot B file and The progress of optimization in D optimization would be based on the energy optimization and rotamer Configuration the violation profiles are provided in the V file the initial model that is generated as I just mentioned Is in the INI file the restraints which the user may impose on the predicted structure are in this file and The schedule for the optimization process is given here. So these are some of the output files That are given out Besides using modeler if you don't know Python then you can go for the Swiss model Swiss model software is a very easy to use software and you can do all of this exercise of homology modeling using the graphical user interface it is available here and Of course, there are other tools which you can explore such as Robeta 3d jigsaw and fire The links for each one of them are provided here so in conclusion Homology modeling is a lengthy process and the pipeline contains several steps Modeler can help you to predict the structures from sequences by using these Several steps in order. However, because it involves Python programming Which you may not know you can go for the Swiss model software as well and You can do it in an automated and graphical way only