NDLI: Proteome-wide prediction of overlapping small molecule and protein binding sites using structure

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Proteome-wide prediction of overlapping small molecule and protein binding sites using structure

Back cover

Molecular BioSystems Vol -6

Molecular BioSystems Vol -5

Molecular BioSystems Vol -4

Molecular BioSystems Vol -3

Molecular BioSystems Vol -2

Proteome-wide prediction of overlapping small molecule and protein binding sites using structure

Content Provider	Royal Society of Chemistry (RSC)
Author	Davis, Fred P.
Copyright Year	2011
Abstract	Small molecules that modulate protein–protein interactions are of great interest for chemical biology and therapeutics. Here I present a structure-based approach to predict ‘bi-functional’ sites able to bind both small molecule ligands and proteins, in proteins of unknown structure. First, I develop a homology-based annotation method that transfers binding sites of known three-dimensional structure onto protein sequences, predicting residues in ligand and protein binding sites with estimated true positive rates of 98% and 88%, respectively, at 1% false positive rates. Applying this method to the human proteome predicts 8463 proteins with bi-functional residues and correctly recovers the targets of known interaction modulators. Proteins with significantly (p < 0.01) more bi-functional residues than expected were found to be enriched in regulatory and depleted in metabolism functions. Finally, I demonstrate the utility of the method by describing examples of predicted overlap and evidence of their biological and therapeutic relevance. The results suggest that combining the structures of known binding sites with established fold detection algorithms can predict regions of protein–protein interfaces that are amenable to small molecule modulation. Open-source software and the results for several complete proteomes are available at http://pibase.janelia.org/homolobind.
Starting Page	545
Ending Page	557
Page Count	13
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	7
Issue Number	2
Journal	Molecular BioSystems
DOI	10.1039/c0mb00200c
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	False positives and false negatives Ligand Proteome Open-source software Molecular biology Metabolism Protein
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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