I am curious if there exist any bioinformatics tools that can predict changes in secondary structure for proteins and/or nucleic acids. For instance, say a C-terminal loop on a protein reorganizes into a helix in response to binding to RNA. Or say an intrinsically unstructured segment of RNA forms a transient stem-loop in order to bind to a protein. Are there any computational tools that could predict such a change short of performing in-lab experiments?
You can use secondary structure prediction servers such as PSIPRED and JPred. You can combine this information with homology modelling and disordered region prediction.
You can use secondary structure prediction servers such as PSIPRED and JPred. You can combine this information with homology modelling and disordered region prediction.
Please follow the link of ExPASy (Bioinformatic resource portal)
https://www.expasy.org/proteomics/protein_structure
You can use PSIPRED and JPred . Besides Momecular Dynamics softwares can be used.
http://ambermd.org/
www.gromacs.org/
www.charmm.org/
There is much software for predicting protein secondary structure, such as PSIPRED, Jpred3, SSpro, PSSpred, PREDICTPROTEIN, PREDATOR, GOR V, and so on. My favorite online tool is PSIPRED. Moreover, Mfold (http://unafold.rna.albany.edu/?q=mfold) is a good choice for predicting RNA secondary structure.
The best way to predict all changes associated with secondary alteration in your protein backbone is to run the molecular dynamic simulation. Two tools including Gromacs and Amber can support you for this idea. NAMD and LAMMPS are two other practical tools in the term of prediction biochemical changes within a biomolecule.
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