3 d protein structure predcition

Question

[geethus2009]

can anyone tell me what are different steps to follows to predict 3d protein structure [ template-based modeling approach in homologous - target ]

thank you in advance your support makes me to learn faster

Answer 1

[tothepoint]

First Identify the template and blast against the database (BLASTp). Check the coverage, evalue, identity if similarity found more that 40% choose the top hits from the blast results. Choose 5+ template (prefer) and align them to query sequence. (These step performed in Modeller) Following alignment series of steps to be performed:

Backbone generation.

Loop Modeling.

Side Chain Modeling.

Model Optimization.

Model Validation (Validation could be performed with various available server Saves, ProQ, ProSA etc. For better understanding this is the general workflow in the figure.