Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field
Protein-ligand docking is currently an important tool in drug discovery efforts and an active area of research
that has been the subject of important developments over the last decade. These are well portrayed in the rising number of
available protein-ligand docking software programs, increasing level of sophistication of its most recent applications, and
growing number of users. While starting by summarizing the key concepts in protein-ligand docking, this article presents
an analysis of the evolution of this important field of research over the past decade. Particular attention is given to the
massive range of alternatives, in terms of protein-ligand docking software programs currently available. The emerging
trends in this field are the subject of special attention, while old established docking alternatives are critically revisited.
Current challenges in the field of protein-ligand docking such as the treatment of protein flexibility, the presence of structural
water molecules and its effect in docking, and the entropy of binding are dissected and discussed, trying to anticipate
the next years in the field.
Keywords: Docking, drug design, entropy, flexibility, scoring, software, virtual Screening.
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