Protein Annotation and Prediction
Improving N terminal protein annotation of Plasmodium species based on signal peptide prediction of orthologous proteins
... The reannotations being proposed redefine the sets of proteins that are targeted to the ER of Plasmodium organisms and are highly relevant, since protein traffick- ing is crucial for the successful development of ...
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A Combined Approach for Genome Wide Protein Function Annotation/Prediction
... In this section, we compare our method with other techniques that also integrate multiple sources of infor- mation for protein annotation. The first technique we compare with is presented by S. Jaeger ’s et ...
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A Combined Approach for Genome Wide Protein Function Annotation/Prediction
... In this section, we compare our method with other techniques that also integrate multiple sources of infor- mation for protein annotation. The first technique we compare with is presented by S. Jaeger ’s et ...
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A combined approach for genome wide protein function annotation/prediction
... In this section, we compare our method with other techniques that also integrate multiple sources of infor- mation for protein annotation. The first technique we compare with is presented by S. Jaeger ’ s ...
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Sequence based feature prediction and annotation of proteins
... of annotation - in other words, which features can be predicted without knowing or explicitly predicting the three-dimensional structure of the protein under ...such protein-annotation ...The ...
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Combining learning and constraints for genome-wide protein annotation
... Our results show that both hierarchical and term- interaction rules contribute in increasing prediction qual- ity in all GO hierarchies, especially for the lower levels where less training examples are available. ...
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Protein annotation and modelling servers at University College London
... new protein sequences outstrips the rate at which new protein structures are de- posited in the public databases, there will be a continued need for accurate protein structure ...function ...
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Protein structure prediction and structure-based protein function annotation
... of protein models, full-atomic models are constructed by REMO 33 from these cluster centroids, while optimizing the hydrogen- bonding network, where a H-bonding list is pre-constructed based on secondary structure ...
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Protein function annotation using protein domain family resources
... function annotation transfer from close homologs is limited (see Figure 4b for Precision-Recall graph as in CAFA ...Function Prediction Special Interest Group (AFP-SIG), which aims to provide large-scale ...
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Exploiting Complex Protein Domain Networks for Protein Function Annotation
... The following methods are widely used EC prediction methods that use combined approaches based on machine learning, sequence encoding, functional domain simi- larity and structural similarity. In DEEPre [18], a ...
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Protein function annotation by homology based inference
... reliable prediction of the structure of a protein from its sequence would almost automatically provide infor- mation about its ...the protein space ...of protein parts to a more profound ...
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Incorporating Gene Annotation into Genomic Prediction of Complex Phenotypes
... gene annotation to define haplotypes in both numerical dosage and categorical effect ...the protein-coding genes (and thus the corresponding pro- teins) including their regulatory regions as biologically ...
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TransATH: Transporter prediction via annotation transfer by homology
... proteins, annotation transfer by homology, subcellular ...(Gene- Protein-Reaction) associations for transport in the reconstruction of metabolic ...transmembrane protein that performs the movement of ...
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An efficient method for protein function annotation based on multilayer protein networks
... In conclusion, many computational methods that inte- grate heterogeneous data for predicting protein (or gene) functions have been suggested. Most of these techniques follow the same basic paradigm: firstly, they ...
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Overview of the protein protein interaction annotation extraction task of BioCreative II
... interaction annotation) showed a similar out- come, with a very high recall of ...to protein interaction-related abstracts that nonetheless do not have corresponding pro- tein-protein interactions ...
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Protein-protein interface: database, analysis and prediction
... of protein-protein interaction have been developed in recent ...of protein domains with data deduced from Protein Data Bank (PDB) (14), ...of protein-protein interfaces, ...of ...
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BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation
... enhanced data selection step. Manually curated annotations from Swiss-Prot are used as reliable source for function prediction of enzymes observed on protein level. The pool of sequences is extended by ...
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A meta-approach for improving the prediction and the functional annotation of ortholog groups
... is annotation, what is important is not to have the largest possible groups, but to ensure that the genes that are in the same group will share the same ...unassigned protein is com- pared to the profile ...
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A protein structure based annotation of genomes
... Automated annotation systems have been developed previously by ...public annotation systems is to support genome sequencing projects, and to provide up-to-date annotations, whereas the 3D-GEN0M ICS ...
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Learning to extract relations for protein annotation
... The goal of the work reported in this article is to alleviate the burden of developing IE systems. To achieve this goal, we use only sentences. Our problem can be formally defined as follows: given relevant sentences ...
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