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Abstract

In this work, we applied a coarse-grained molecular dynamics method for simulating inhibitors entering the binding cavity of human immunodeficiency virus type 1 protease (HIV-1 PR). It shows that the coarse-grained dynamics, in consistent with the experimental results, can capture the essential binding dynamics of inhibitors into protease. The primary driving force for the binding processes is the non-bond interaction between inhibitors and PR. Meanwhile, the interacting strength between inhibitors and protease, have great influence on the binding processes. This study also provides important guidelines for design of novel inhibitors with optimized binding pathway and fast binding kinetics