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Keywords {🔍}

methods, terms, cafa, threshold, measure, leaf, term, protein, prediction, function, score, method, priors, annotations, predicted, set, top, article, psiblast, figure, proteins, recall, experimental, hits, pubmed, annotation, data, predictions, bpo, precision, blast, performance, google, scholar, measures, mfo, leaves, swissprot, homologybased, number, postcafa, gotcha, reliability, target, inference, baseline, scores, table, studenta, ontology,

Topics {✒️}

biological process ontology marti-renom ma florian auer rule-based protein annotator homology-based inference sets /bmcbioinformatics/supplements/14/s3 simple homology-based inference biological process membrane protein structure open access article article number s7 functional keywords diverse nearest-neighbor methods k-nearest-neighbor approach basic homology-inference methods maintaining excellent databases article download pdf homology-based methods fared meta classifier [13] single-function aldolase enzyme returned psi-blast e-values homology-based inference predict protein function homology-based method ranks author information authors post-cafa parameter optimization full size image random swiss-prot protein nearest-neighbor principles protein function assessed optimization process protein function prediction protein function prediction typical swiss-prot annotations multiple psi-blast hits privacy choices/manage cookies entire psi-blast query imply high accuracy/precision nucleic acids research artificial intelligence research homology-based methods homology-based predictors molecular function ontology post-cafa optimization baseline background full size table universal protein resource author correspondence cellular component ontology top psi-blast hits

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WebPage:
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         headline:Homology-based inference sets the bar high for protein function prediction
         description:Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference. Here, we describe a few methods that predict protein function exclusively through homology. Together, they set the bar or lower limit for future improvements. During the development of these methods, we faced two surprises. Firstly, our most successful implementation for the baseline ranked very high at CAFA1. In fact, our best combination of homology-based methods fared only slightly worse than the top-of-the-line prediction method from the Jones group. Secondly, although the concept of homology-based inference is simple, this work revealed that the precise details of the implementation are crucial: not only did the methods span from top to bottom performers at CAFA, but also the reasons for these differences were unexpected. In this work, we also propose a new rigorous measure to compare predicted and experimental annotations. It puts more emphasis on the details of protein function than the other measures employed by CAFA and may best reflect the expectations of users. Clearly, the definition of proper goals remains one major objective for CAFA.
         datePublished:2013-02-28T00:00:00Z
         dateModified:2013-02-28T00:00:00Z
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            Threshold Measure
            Experimental Annotation
            Predict Protein Function
            Biological Process Ontology
            Baseline Classifier
            Bioinformatics
            Microarrays
            Computational Biology/Bioinformatics
            Computer Appl. in Life Sciences
            Algorithms
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      headline:Homology-based inference sets the bar high for protein function prediction
      description:Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference. Here, we describe a few methods that predict protein function exclusively through homology. Together, they set the bar or lower limit for future improvements. During the development of these methods, we faced two surprises. Firstly, our most successful implementation for the baseline ranked very high at CAFA1. In fact, our best combination of homology-based methods fared only slightly worse than the top-of-the-line prediction method from the Jones group. Secondly, although the concept of homology-based inference is simple, this work revealed that the precise details of the implementation are crucial: not only did the methods span from top to bottom performers at CAFA, but also the reasons for these differences were unexpected. In this work, we also propose a new rigorous measure to compare predicted and experimental annotations. It puts more emphasis on the details of protein function than the other measures employed by CAFA and may best reflect the expectations of users. Clearly, the definition of proper goals remains one major objective for CAFA.
      datePublished:2013-02-28T00:00:00Z
      dateModified:2013-02-28T00:00:00Z
      pageStart:1
      pageEnd:10
      license:https://creativecommons.org/licenses/by/2.0
      sameAs:https://doi.org/10.1186/1471-2105-14-S3-S7
      keywords:
         Threshold Measure
         Experimental Annotation
         Predict Protein Function
         Biological Process Ontology
         Baseline Classifier
         Bioinformatics
         Microarrays
         Computational Biology/Bioinformatics
         Computer Appl. in Life Sciences
         Algorithms
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            name:Tobias Hamp
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         name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
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      name:TUM, Department of Informatics, Bioinformatics & Computational Biology
      address:
         name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
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      name:TUM, Department of Informatics, Bioinformatics & Computational Biology
      address:
         name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
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      name:TUM, Department of Informatics, Bioinformatics & Computational Biology
      address:
         name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
         type:PostalAddress
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology
      address:
         name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
         type:PostalAddress
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology
      address:
         name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
         type:PostalAddress
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology
      address:
         name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
         type:PostalAddress
      name:Institute of Advanced Study (TUM-IAS) Lichtenbergstr. 2a
      address:
         name:Institute of Advanced Study (TUM-IAS) Lichtenbergstr. 2a, Garching/Munich, Germany
         type:PostalAddress
      name:New York Consortium on Membrane Protein Structure (NYCOMPS) & Department of Biochemistry and Molecular Biophysics Columbia University
      address:
         name:New York Consortium on Membrane Protein Structure (NYCOMPS) & Department of Biochemistry and Molecular Biophysics Columbia University, New York, USA
         type:PostalAddress
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Person:
      name:Tobias Hamp
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Rebecca Kassner
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Stefan Seemayer
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Esmeralda Vicedo
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Christian Schaefer
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Dominik Achten
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
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      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Ariane Boehm
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Tatjana Braun
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Maximilian Hecht
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Mark Heron
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Peter Hönigschmid
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Thomas A Hopf
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Stefanie Kaufmann
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Michael Kiening
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Denis Krompass
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Cedric Landerer
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Yannick Mahlich
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Manfred Roos
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
      name:Burkhard Rost
      affiliation:
            name:TUM, Department of Informatics, Bioinformatics & Computational Biology
            address:
               name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
            name:Institute of Advanced Study (TUM-IAS) Lichtenbergstr. 2a
            address:
               name:Institute of Advanced Study (TUM-IAS) Lichtenbergstr. 2a, Garching/Munich, Germany
               type:PostalAddress
            type:Organization
            name:New York Consortium on Membrane Protein Structure (NYCOMPS) & Department of Biochemistry and Molecular Biophysics Columbia University
            address:
               name:New York Consortium on Membrane Protein Structure (NYCOMPS) & Department of Biochemistry and Molecular Biophysics Columbia University, New York, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:TUM, Department of Informatics, Bioinformatics & Computational Biology, Garching/Munich, Germany
      name:Institute of Advanced Study (TUM-IAS) Lichtenbergstr. 2a, Garching/Munich, Germany
      name:New York Consortium on Membrane Protein Structure (NYCOMPS) & Department of Biochemistry and Molecular Biophysics Columbia University, New York, USA

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