2013
DOI: 10.1371/journal.pcbi.1003341
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Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

Abstract: A challenge in structural genomics is prediction of the function of uncharacterized proteins. When proteins cannot be related to other proteins of known activity, identification of function based on sequence or structural homology is impossible and in such cases it would be useful to assess structurally conserved binding sites in connection with the protein's function. In this paper, we propose the function of a protein of unknown activity, the Tm1631 protein from Thermotoga maritima, by comparing its predicte… Show more

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Cited by 47 publications
(47 citation statements)
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“…Prior to the recent accumulation of RNA-seq data, protein structure methods [6975], based on the assumption that structural differences may predispose isoforms to functional diversification, had been the main route for predicting isoform functions. These methods are based on amino acid sequences, protein domains, and 3D conformational structures (Figure 2).…”
Section: Emerging Computational Approaches For Predicting Isoform Funmentioning
confidence: 99%
“…Prior to the recent accumulation of RNA-seq data, protein structure methods [6975], based on the assumption that structural differences may predispose isoforms to functional diversification, had been the main route for predicting isoform functions. These methods are based on amino acid sequences, protein domains, and 3D conformational structures (Figure 2).…”
Section: Emerging Computational Approaches For Predicting Isoform Funmentioning
confidence: 99%
“…Structure-based function prediction approaches include docking and template-based structural modelling [71 ,72], detection of geometric and physicochemical similarities among functional sites [73][74][75][76], and structural alignment. These approaches have been successful in predicting a wide range of new protein functions/interactions including enzymatic functions [69,70 ,77], binding sites [78,79], protein-DNA interactions [76,80], and protein-protein complexes [68,71 ].…”
Section: Structure-based Function Discoverymentioning
confidence: 99%
“…These approaches have been successful in predicting a wide range of new protein functions/interactions including enzymatic functions [69,70 ,77], binding sites [78,79], protein-DNA interactions [76,80], and protein-protein complexes [68,71 ]. In an exciting recent example of structure-based function prediction, Zhang et al…”
Section: Structure-based Function Discoverymentioning
confidence: 99%
“…Possible interactions of a protein with ligands are thus taken into account. A structural similarity search algorithm, which uses a fast maximum clique algorithm [20] and operates independently of fold and sequence, performs a local, surface-oriented comparison of the proteins represented as graphs. All possible similar regions between two compared proteins are identified.…”
Section: Overview Of the Probis Algorithmmentioning
confidence: 99%
“…Particularly, we plan to parallelize the maximum clique algorithm, [20] which is the essential building block of the proposed protein structural comparisons. We will explore the efficiency of many-core and graphic processing unit (GPU) platforms in further parallelization approaches.…”
Section: Software News and Updates Wwwc-chemorgmentioning
confidence: 99%