Comparison of OTUB1 (DUB) and CNOT4 (E3) binding sites on
A web server for analysis, comparison and prediction of protein ligand binding sites
... The propensity scores of various ligands are calcu- lated, and the regions of all the protein sequences are highlighted on the basis of propensity scores. The propensity-based method can predict the probable inter- ...
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Pipeline for Efficient Mapping of Transcription Factor Binding Sites and Comparison of Their Models
... Chapter I: Introduction and Background Genes are parts of DNA and their activation requires a combinatorial and synergistic activity of a group of regulatory proteins and polymerases [1]. One class of such regulatory ...
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Prediction of DNA-Binding Proteins and their Binding Sites
... structural comparison protocol and the other employs a sequence comparison ...structural comparison protocol detects significant structural similarity between the query and a template known to bind ...
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A Structural Comparison Approach for Identifying Small Variations in Binding Sites of Homologous Proteins
... from binding to the other ...strong binding in ...possible sites where drug design could be directly applied in order to selectively target ...
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Methods for the Efficient Comparison of Protein Binding Sites and for the Assessment of Protein-Ligand Complexes
... an even higher average AUC, which is 0.96 and clearly demonstrates that RAPMAD can be used as a tool to seek for putative cross-reactivity. 5.3.6 Identification of New Ligands for the NMDA Receptor Stimulated by the ...
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Fuzzy Modeling of Labeled Point Cloud Superposition for the Comparison of Protein Binding Sites
... small molecules bind to these sites and cause a reaction of the protein pharmaceutical chemistry is interested in binding sites and similarity measures between them.. I inhibit binding s[r] ...
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Fuzzy Modeling of Labeled Point Cloud Superposition for the Comparison of Protein Binding Sites
... Email: {thomas,eyke}@mathematik.uni-marburg.de Abstract— Geometric objects are often represented approxi- mately in terms of a finite set of points in three-dimensional Eu- clidean space. In this paper, we extend this ...
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Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites
... MyoD binding sites might not be occupied 100% of the time at endogenous levels of MyoD, although this re- mains speculative since other unknown variables might have affected the ChIP efficiencies or ...
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CaMELS : In silicoprediction of calmodulin binding proteins and their binding sites
... dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and ...their binding ...
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Comparison of Ligand Binding Affinities at Human 11-Imidazoline Binding Sites and the High Affinity State of Alpha-2 Adrenoceptor Subtypes1
... To identify selective compounds for nonadrenergic I1-imidazo- line receptors (Ii), the afinities of 22 ligands for [125I]p-iodo- clonidine binding have been compared at human platelet I-[r] ...
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Statistics for Transcription Factor Binding Sites
... Many computational tools deal with ab initio discovery of new PFMs on a set of related sequences (Tompa et al., 2005). Since there is no best method, several programs are usually applied resulting in a redundant set of ...
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Phosphate binding sites identification in protein structures
... During the structural comparison only groups of the same type are matched. We obtained an average of 504.2 predicted PbMs per structure on the training set, using an RMSD threshold of 0.7. We sorted all the PbMs ...
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The design of conducting polymers with metal binding sites
... In comparison to other reported studies, which show four singlets in this region due to the four trimeric conformations, it can be assumed that our polymers contain the required defect free homogeneous ...
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Modeling the Quantitative Specificity of DNA-Binding Proteins from Example Binding Sites
... scoring sites. Sites that had the same scores were allowed to be sorted by Excel and no modification of this ranking was ...of sites ranked at or above the threshold was known in each case and this ...
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Large-Scale Analysis of Protein-Ligand Binding Sites using the Binding MOAD Database.
... within binding pockets across the known “pocketome” and their relative importance in partitioning the vast many-to-many interaction network of proteins and small ...the Binding MOAD database, a vast, ...
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PocketPicker: analysis of ligand binding-sites with shape descriptors
... Comparison of pocket shapes A descriptor was designed to describe the shape of a pocket with respect to the buriedness of the site. Grid probes were grouped into six categories A, B, C, D, E, F holding grid point ...
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PocketPicker: analysis of ligand binding-sites with shape descriptors
... Comparison of pocket shapes A descriptor was designed to describe the shape of a pocket with respect to the buriedness of the site. Grid probes were grouped into six categories A, B, C, D, E, F holding grid point ...
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Variable structure motifs for transcription factor binding sites
... DNA binding sites that is not too restrictive nor ...Our comparison with existing tools shows that on average it does not have better predictive accuracy than existing ...
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Immunohistochemical Study of OTUB1 Expression in Colon Cancer
... Immunohistochemistry staining was carried out following the manufacturer’s protocols. Paraffin sections (4 μm thick) were deparaffined in two changes of xylene for 5 minutes each and then hydrated in decreasing ...
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Multiple high affinity binding sites for
... Molecular biology studies have revealed a very low level of homology between 5-HT 1 and 5-HT 2 receptors, suggesting that these two 5-HT receptor classes diverged early in evolution, perhaps even before the separation of ...
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