We present an efficient approach to search fragment binding modes to a protein. Firstly, binding site is identified by using molecular dynamics (MD) simulation using fragment-mixed solvent. Then, our original method, non-bonding function replica-exchange method (nfREM), is carried out to search binding mode candidates of the fragment at the binding site. Finally, metadynamics is executed to search favorable binding modes in the rationalized sampling space which is estimated from the binding mode candidates information.<br/>We will discuss our approach in detail at the meeting.

Rationalization of sampling space for searching favorable binding modes

2019 Spring National Meeting

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