Curious to see what people would like to see included in the next versions of the I-TASSER and related programs from Zhang lab (including I-TASSER (template based structure prediction), QUARK (template free structure prediction), COFACTOR/COACH (ligand binding prediction/function annotation).
*Note I am not directly involved in the development of any of these programs and this does not represent a promise that the features will be included. This is just a poll to see what new features/areas of improvement could be made and pass along the information to others.
There are still so much issues with the N-terminal modeling in I-Tasser, if it is modeled by ab-initio approach. I think, this is one of the area of improvement required in I-Tasser.
yup also added mutation detection analysis in I-Tasser and need every thing which used for protein modeling like domain analysis, docking sites, active site prediction and protein protein interactions.
@Muhammed A protein-protein docking/structure prediction tool (TACOS) using matches to the protein quaternary structure library is under development. It still has some bugs that are being worked on, so I cannot recommend it at the moment. However, SPRING, http://zhanglab.ccmb.med.umich.edu/spring/ another tool for protein-protein structure prediction, is available.
You can try BSP-SLIM http://zhanglab.ccmb.med.umich.edu/BSP-SLIM/ for docking, which gives a better performance for docking on low resolution structures like the models generated by I-TASSER than AUTO-DOCK. Integrating the docked results into the structure prediction (perturbation of the structure by lignad/cofactor binding) is being worked on.
For domain analysis, you can try ThreaDom http://zhanglab.ccmb.med.umich.edu/ThreaDom/ This is another area that is being worked on.
Can you explain exactly what you mean by mutation analysis?
*Note I am not directly involved in the development of any of these programs and this does not represent a promise that the features will be included. This is just a poll to see what new features/ areas of improvement could be made and pass along the information to others.
@Shishir The N-terminus of many proteins is disordered and not present in many of the structures of the PDB, which represents a problem for template based programs like I-TASSER. You could try QUARK, a template free program, which may be more successful. Out of curiosity, have you had more luck with other programs that you can recommend?
dear Brender,
Need to incorporate protein modeling to visualize the effects of mutations on protein structure in I-TASSER which show how a specific mutation can change protein structure.
I-Tasser is one of the best tools for threading and assembly in the filed of protein structure prediction. I have used it many times and i would use that in my future works as well. I would like to see the better optimized loop positioning in the models. I know the loop prediction and optimization process is very difficult and has many practical problems associated with it. along with that alanine scanning and mutational analysis of a particular residue especially when it is a part of active site or a Binding site of the protein, which can give more insights into the mechanistic part of the protein structure.
Regarding mutant analysis, there is a tool in development that can be adapted for this task. Evodesign http://zhanglab.ccmb.med.umich.edu/EvoDesign/
is a protein design program using evolutionary structural profiles to find sequences that will fold to specified structures. A key step in its algorithm is evaluating the influence of point mutations to see if they are compatible with the target structure. The Evodesign runs this process iteratively over many mutations, however it would not be too difficult to set up a server to look at specified mutations independently.
What would be good properties to look for? Currently it is set up to check stability, but it may be possible to look at thermal stability and other properties. I am working on this specific project, so if you have suggestions I may be able to incorporate them.
I would suppose a tool dedicated to membrane protein prediction would be a great addition to the current ITASSER suite. I have tried to model membrane proteins using the current ITASSER and a lot of tweaking around is needed. Although I must say that I found that ITASSER performed better than servers dedicated to membrane proteins like the MEDELLER suite.
There is a new version of I-TASSER specifically designed for GPCRs that will be online relatively soon I think http://zhanglab.ccmb.med.umich.edu/research/#GPCR. However, since it is specifically for GPCRs and uses a GPCR-specific force-field and structural library, it will not be of much help for generic membrane proteins.
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