Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple Due to Inherent Shape Similarity

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• 作者：Timo Krotzky ; Thomas Rickmeyer ; Thomas Fober ; Gerhard Klebe
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2014
• 出版时间：November 24, 2014
• 年：2014
• 卷：54
• 期：11
• 页码：3229-3237
• 全文大小：432K
• ISSN：1549-960X

文摘

Methods for comparing protein binding sites are frequently validated on data sets of pockets that were obtained simply by extracting the protein area next to the bound ligands. With this strategy, any unoccupied pocket will remain unconsidered. Furthermore, a large amount of ligand-biased intrinsic shape information is predefined, inclining the subsequent comparisons as rather trivial even in data sets that hardly contain redundancies in sequence information. In this study, we present the results of a very simplistic and shape-biased comparison approach, which stress that unrestricted cavity extraction is essential to enable unexpected cross-reactivity predictions among proteins and function annotations of orphan proteins.