Protein Annotation
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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mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
... protein annotation still remains: protein sequences annotation often relies on alignment programs auto- matically retrieving the first hit only ...of protein search databases and ...
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Combining learning and constraints for genome-wide protein annotation
... decomposing it into simpler prediction tasks, and exploits prior biological knowledge to reconcile the resulting pre- dictions. OCELOT instantiates one task for every can- didate GO term, i.e., deciding whether a given ...
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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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HH-suite3 for fast remote homology detection and deep protein annotation.
... without annotation due to the lack of an identifiable, annotated homologous protein [ 1 ...homologous protein with an annotated function or a known structure from which the function or structure of ...
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Protein annotation from protein interaction networks and Gene Ontology
... assign protein functions based on a probabilistic analysis of graph neighborhoods [32–34] ...the annotation of any node was conditionally indepen- dent of all other nodes, given its ...data, protein ...
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The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification.
... to protein motifs, (ii) a searchable interface for these articles, (iii) a tool to clas- sify and rank these articles based on their similarity to the manually curated motif classes in the ELM resource and (iv) an ...
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New in protein structure and function annotation: Hotspots, single nucleotide polymorphisms and the 'Deep Web'
... of protein sequence data continues to widen the gap between available sequences and ...known protein sequences, however, there is detailed knowledge about neither their function nor their ...of ...
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DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe
... or protein functional ...known protein in NCBI-nr, NCBI-env and CAZy ...the protein annotation? For enzymes, there is a well-established system, the Enzyme Commis- sion (EC) number [14], which ...
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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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Application of text-mining for updating protein post-translational modification annotation in UniProtKB
... for protein phosphorylation information extraction ...of protein phosphorylation, such as protein inter- action induced by phosphorylation ...
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Development and Application of Bovine and Porcine Oligonucleotide Arrays with Protein-Based Annotation
... Journal of Biomedicine and Biotechnology 3 to Btau2.0. After aligning the homologous vertebrate pro- teins to the bovine genome using Exonerate, the 36,547 EST clusters could be grouped to form 16,849 unique gene loci. ...
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HAMAP in 2013, new developments in the protein family classification and annotation system
... genome annotation, providing contextual information that is complementary to the primary sequence and that can be used to infer potential new functions for uncharacterized genes ...genome annotation, both ...
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Comparison of Protein Active Site Structures for Functional Annotation of Proteins and Drug Design
... hypothetical protein determined by comparison against the CPASS database would identify the protein(s) that has the highest probability of sharing a similar function with the hypothetical ...
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A clustering method for robust and reliable large scale functional and structural protein sequence annotation
... crucial. Protein sequence annotation is challenging and, due to the size of the problem, only computational approaches can provide a feasible ...for protein automatic large-scale annotation, ...
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Application of text-mining for updating protein post-translational modification annotation in UniProtKB.
... Our information extraction method integrates bio- logical knowledge in the form of expert-curated patterns and domain-specific rules. Since it only relies on a spe- cific vocabulary, the method can be easily extended to ...
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Annotation and characterization of the Plasmodium vivax rhoptry neck protein 4 (Pv RON4)
... regarding protein length (see Additional file 1), mainly due to large deletions bet- ween residues 179-305 where the TRs ...circumsporozoite protein (CSP) consists of a central repeat region, which is ...
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Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
... The second peptide, "TDLLPIMK", was found to match the cytoplasmic B. melitensis keto-hydroxyglutarate- aldolase (BMEII0009) and then assigned to BAB2_0083 in B. abortus 2308. This peptide overlaps the region ...
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