Literature DB >> 18037900

Predicting protein function from sequence and structure.

David Lee1, Oliver Redfern, Christine Orengo.   

Abstract

While the number of sequenced genomes continues to grow, experimentally verified functional annotation of whole genomes remains patchy. Structural genomics projects are yielding many protein structures that have unknown function. Nevertheless, subsequent experimental investigation is costly and time-consuming, which makes computational methods for predicting protein function very attractive. There is an increasing number of noteworthy methods for predicting protein function from sequence and structural data alone, many of which are readily available to cell biologists who are aware of the strengths and pitfalls of each available technique.

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Year:  2007        PMID: 18037900     DOI: 10.1038/nrm2281

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  177 in total

1.  From complete genome sequence to 'complete' understanding?

Authors:  Michael Y Galperin; Eugene V Koonin
Journal:  Trends Biotechnol       Date:  2010-08       Impact factor: 19.536

2.  The annotation of full zinc proteomes.

Authors:  Ivano Bertini; Leonardo Decaria; Antonio Rosato
Journal:  J Biol Inorg Chem       Date:  2010-05-05       Impact factor: 3.358

3.  Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation.

Authors:  A D Wilkins; R Lua; S Erdin; R M Ward; O Lichtarge
Journal:  Protein Sci       Date:  2010-07       Impact factor: 6.725

4.  Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.

Authors:  Huiying Zhao; Yuedong Yang; Yaoqi Zhou
Journal:  Bioinformatics       Date:  2010-06-04       Impact factor: 6.937

5.  Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification.

Authors:  Benoit H Dessailly; Oliver C Redfern; Alison L Cuff; Christine A Orengo
Journal:  Structure       Date:  2010-11-10       Impact factor: 5.006

Review 6.  Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Authors:  Khader Shameer; Lokesh P Tripathi; Krishna R Kalari; Joel T Dudley; Ramanathan Sowdhamini
Journal:  Brief Bioinform       Date:  2015-10-22       Impact factor: 11.622

7.  Interregional Coevolution Analysis Revealing Functional and Structural Interrelatedness between Different Genomic Regions in Human Mastadenovirus D.

Authors:  Gabriel Gonzalez; Kanako O Koyanagi; Koki Aoki; Hidemi Watanabe
Journal:  J Virol       Date:  2015-04-01       Impact factor: 5.103

8.  Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery-a structure-based approach.

Authors:  Vishwanath Ramatenki; Ramakrishna Dumpati; Rajender Vadija; Santhiprada Vellanki; Sarita Rajender Potlapally; Rohini Rondla; Uma Vuruputuri
Journal:  J Chem Biol       Date:  2016-12-24

9.  Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Authors:  Fang-Yu Lin; Jing Huang; Poonam Pandey; Chetan Rupakheti; Jing Li; Benoı T Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-04-27       Impact factor: 6.006

10.  In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells.

Authors:  Noor Nahar; Aminur Rahman; Maria Moś; Tomasz Warzecha; Sibdas Ghosh; Khaled Hossain; Neelu N Nawani; Abul Mandal
Journal:  J Mol Model       Date:  2014-02-20       Impact factor: 1.810

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