Profacgen makes use of state-of-the-art docking software tools to find the relative transformation and conformation of the protein and nucleic acid involved in energetically favorable complex formation. The general procedures are: First, a rigid body global search is performed and geometrically plausible protein–nucleic acid complex structures are generated. In this process, user-defined restraints can be applied to limit the search space. The resulting models are scored and ranked using statistical potentials, developed specifically for protein–RNA or protein–DNA complexes. The best-scored structures are then clustered and representatives of the largest clusters are selected for structural optimization by energy minimization before being presented to the customer.

https://www.profacgen.com/Protein-Nucleic-Acid-Docking.htm

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