ArticleJournal of molecular biology2007
Towards fully automated structure-based function prediction in structural genomics: a case study.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Predicting Protein Function in the AI and Big Data Era.Biochemistry · 2025Review
- Functional prediction of proteins from the human gut archaeome.ISME communications · 2024Article
- Isolation, characterization and in silico analysis of 3-Hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) gene from Andrographis paniculata (Burm. f) Nees.Molecular biology reports · 2020Article
- A Novel Geometry-Based Approach to Infer Protein Interface Similarity.Scientific reports · 2018Article
- Functional Prediction of Hypothetical Transcription Factors ofComputational and structural biotechnology journal · 2018Article
- The impact of structural genomics: the first quindecennial.Journal of structural and functional genomics · 2016Review
- Characterization and structure prediction of partial length protein sequences of pcoA, pcoR and chrB genes from heavy metal resistant bacteria from the Klip River, South Africa.International journal of molecular sciences · 2015Article
- Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.Biochemistry · 2015Article
- Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases.Frontiers in bioengineering and biotechnology · 2015Article
- Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks.The Plant cell · 2014Article
- Structure prediction of partial-length protein sequences.International journal of molecular sciences · 2013Article
- Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.Methods in molecular biology (Clifton, N.J.) · 2012Article
- ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree.Nucleic acids research · 2012Article
- Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns.BMC genomics · 2011Article
- The Protein Maker: an automated system for high-throughput parallel purification.Acta crystallographica. Section F, Structural biology and crystallization communications · 2011Article
- Maps of protein structure space reveal a fundamental relationship between protein structure and function.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Protein function prediction: towards integration of similarity metrics.Current opinion in structural biology · 2011Review
- Structural analysis of heme proteins: implications for design and prediction.BMC structural biology · 2011Article
- 1,000 structures and more from the MCSG.BMC structural biology · 2011Article
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9 authors.
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Abstract
As the global Structural Genomics projects have picked up pace, the number of structures annotated in the Protein Data Bank as hypothetical protein or unknown function has grown significantly. A major challenge now involves the development of computational methods to assign functions to these proteins accurately and automatically. As part of the Midwest Center for Structural Genomics (MCSG) we have developed a fully automated functional analysis server, ProFunc, which performs a battery of analyses on a submitted structure. The analyses combine a number of sequence-based and structure-based methods to identify functional clues. After the first stage of the Protein Structure Initiative (PSI), we review the success of the pipeline and the importance of structure-based function prediction. As a dataset, we have chosen all structures solved by the MCSG during the 5 years of the first PSI. Our analysis suggests that two of the structure-based methods are particularly successful and provide examples of local similarity that is difficult to identify using current sequence-based methods. No one method is successful in all cases, so, through the use of a number of complementary sequence and structural approaches, the ProFunc server increases the chances that at least one method will find a significant hit that can help elucidate function. Manual assessment of the results is a time-consuming process and subject to individual interpretation and human error. We present a method based on the Gene Ontology (GO) schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment.
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