Enzyme Nomenclature. Recommendations 1984

Webb, Edwin C.

doi:10.1111/j.1432-1033.1989.tb14579.x

Cited by 33 publications

(6 citation statements)

References 363 publications

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“…The physiological substrate of paraoxonase remains unknown. The results reported here support the contention of Gan et al (1991) that a separate classification for paraoxonase (Webb, 1989)…”

Section: Discussionsupporting

confidence: 92%

Purification of rabbit and human serum paraoxonase

Furlong¹,

Richter²,

Chapline³

et al. 1991

Biochemistry

125

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Rabbit serum paraoxonase/arylesterase has been purified to homogeneity by Cibacron Blue-agarose chromatography, gel filtration, DEAE-Trisacryl M chromatography, and preparative SDS gel electrophoresis. Renaturation (Copeland et al., 1982) and activity staining of the enzyme resolved by SDS gel electrophoresis allowed for identification and purification of paraoxonase. Two bands of active enzyme were purified by this procedure (35,000 and 38,000). Enzyme electroeluted from the preparative gels was reanalyzed by analytical SDS gel electrophoresis, and two higher molecular weight bands (43,000 and 48,000) were observed in addition to the original bands. This suggested that repeat electrophoresis resulted in an unfolding or other modification and slower migration of some of the purified protein. The lower mobility bands stained weakly for paraoxonase activity in preparative gels. Bands of each molecular weight species were electroblotted onto PVDF membranes and sequenced. The gas-phase sequence analysis showed that both the active bands and apparent molecular weight bands had identical amino-terminal sequences. Amino acid analysis of the four electrophoretic components from PVDF membranes also indicated compositional similarity. The amino-terminal sequences are typical of the leader sequences of secreted proteins. Human serum paraoxonase was purified by a similar procedure, and ten residues of the amino terminus were sequenced by gas-phase procedures. One amino acid difference between the first ten residues of human and rabbit was observed.

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Section: Discussionsupporting

confidence: 92%

Purification of rabbit and human serum paraoxonase

Furlong¹,

Richter²,

Chapline³

et al. 1991

Biochemistry

125

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“…5. Moreover, for the version of FunFOLD (FunFOLD3) integrated into the IntFOLD pipeline [46], putative EC [44] and GO [45] codes, derived from templates used in the prediction from the BioLip [41] database are included. (See Note 3 for details on the IntFOLD server [46,55]).…”

Section: How To Interpret the Resultsmentioning

confidence: 99%

“…Another major change in FunFOLD3 is the use of the BioLip database [41], for the determination of biologically relevant ligands at multiple binding sites. In addition to the provision of functional annotations, namely EC [44] numbers and GO terms [45]. The FunFOLD3 algorithm along with FunFOLDQA [1] have been integrated into the latest version of the IntFOLD server pipeline [46] and is available as an executable JAR file.…”

Section: The Funfold3 Algorithm For the Prediction Of Protein-ligand Interactionsmentioning

confidence: 99%

In silico Identification and Characterization of Protein-Ligand Binding Sites

Roche

McGuffin

2016

Methods in Molecular Biology

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Protein-ligand binding site prediction methods aim to predict, from amino acid sequence, protein-ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein-ligand interactions has become extremely important to help determine a protein's functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein-ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein-ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein-ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.

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“…Ideally, proteins of the same or closely related functions ought to be assigned in the same cluster. We considered the Enzyme Commission (EC) number classification of enzymes [19], and color coded the EC numbers such that closely related functions were given similar colors, as provided in http://pitgroup.org/seqclust/bsites_AAcodes/EC_colour.html.…”

Section: Resultsmentioning

confidence: 99%

A hybrid clustering of protein binding sites

2010

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The Protein Data Bank contains the description of approximately 27 000 protein–ligand binding sites. Most of the ligands at these sites are biologically active small molecules, affecting the biological function of the protein. The classification of their binding sites may lead to relevant results in drug discovery and design. Clusters of similar binding sites were created here by a hybrid, sequence and spatial structure‐based approach, using the OPTICS clustering algorithm. A dissimilarity measure was defined: a distance function on the amino acid sequences of the binding sites. All the binding sites were clustered in the Protein Data Bank according to this distance function, and it was found that the clusters characterized well the Enzyme Commission numbers of the entries. The results, carefully color coded by the Enzyme Commission numbers of the proteins, containing the 20 967 binding sites clustered, are available as html files in three parts at http://pitgroup.org/seqclust/.

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Enzyme Nomenclature. Recommendations 1984

Cited by 33 publications

References 363 publications

Purification of rabbit and human serum paraoxonase

Purification of rabbit and human serum paraoxonase

In silico Identification and Characterization of Protein-Ligand Binding Sites

A hybrid clustering of protein binding sites

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