Generally any model structure is 6-8 angstrom from native when there is low similarity but for drug designer it is not helpful. Is there any way to get a better structure at least lower rmsd when the native structure is not known either through MD or any refinement. Any literature suggestions will also be helpful or any group working on these problems.
Hi Ashutosh
Get in touch with the bioinformatics departments in India or abroad ..who are involved in this type of analysis...such as IMTECH chandigarh etc...they will be the best people to give you appropriate advice....but at the end...the model should also fit well with the wet lab validation experiments..bye
Hi
It is based on template. As much template will be homologous to query sequence, model will be of better quality. Structure refinement by MD simulation is based on starting structure if structure is not close to native structure before MD simulation you wont get structure close to native after MD simulation.
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