Over the past ten years, the number of three-dimensional protein structures identified by advanced
science and technology increases, and the gene information becomes more available than ever
before as well. The development of computing science becomes another driving force which makes it
possible to use computational methods effectively in various phases of the drug design and research.
Now Structure-Based Drug Design (SBDD) tools are widely used to help researchers to predict the position
of small molecules within a three-dimensional representation of the protein structure and estimate
the affinity of ligands to target protein with considerable accuracy and efficiency. They also accelerate
discovery speed of potent drug and reduce the cost and times for drug research. Here we present an
overview of SBDD used in drug discovery and highlight its recent successes and major challenges to
current SBDD methodologies.
Keywords: Drug design, SBDD, Molecular docking, Scoring function, Target flexibility, Solvation effect.
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