Literature DB >> 22095055

Proteins: form and function.

Roy D Sleator1.   

Abstract

An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; which has in turn facilitated an expanse of functional derivatives. Herein, I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed.

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Year:  2012        PMID: 22095055      PMCID: PMC3357337          DOI: 10.4161/bbug.18303

Source DB:  PubMed          Journal:  Bioeng Bugs        ISSN: 1949-1018


  57 in total

1.  Increased coverage of protein families with the blocks database servers.

Authors:  J G Henikoff; E A Greene; S Pietrokovski; S Henikoff
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  From protein structure to biochemical function?

Authors:  Roman A Laskowski; James D Watson; Janet M Thornton
Journal:  J Struct Funct Genomics       Date:  2003

3.  Enzyme function less conserved than anticipated.

Authors:  Burkhard Rost
Journal:  J Mol Biol       Date:  2002-04-26       Impact factor: 5.469

Review 4.  Structural genomics: computational methods for structure analysis.

Authors:  Sharon Goldsmith-Fischman; Barry Honig
Journal:  Protein Sci       Date:  2003-09       Impact factor: 6.725

5.  FATCAT: a web server for flexible structure comparison and structure similarity searching.

Authors:  Yuzhen Ye; Adam Godzik
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

Review 6.  Duplication, divergence and formation of novel protein topologies.

Authors:  Christine Vogel; Veronica Morea
Journal:  Bioessays       Date:  2006-10       Impact factor: 4.345

7.  Semantic data integration and knowledge management to represent biological network associations.

Authors:  Sascha Losko; Klaus Heumann
Journal:  Methods Mol Biol       Date:  2009

8.  Crystal structure determination, refinement and molecular model of creatine amidinohydrolase from Pseudomonas putida.

Authors:  H W Hoeffken; S H Knof; P A Bartlett; R Huber; H Moellering; G Schumacher
Journal:  J Mol Biol       Date:  1988-11-20       Impact factor: 5.469

9.  Volume changes in protein evolution.

Authors:  M Gerstein; E L Sonnhammer; C Chothia
Journal:  J Mol Biol       Date:  1994-03-04       Impact factor: 5.469

10.  PAST: fast structure-based searching in the PDB.

Authors:  Hanjo Täubig; Arno Buchner; Jan Griebsch
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

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  10 in total

Review 1.  Under the microscope: From pathogens to probiotics and back.

Authors:  Roy D Sleator
Journal:  Bioengineered       Date:  2015       Impact factor: 3.269

2.  The genetic code. Rewritten, revised, repurposed.

Authors:  Roy D Sleator
Journal:  Artif DNA PNA XNA       Date:  2014

Review 3.  A beginner's guide to phylogenetics.

Authors:  Roy D Sleator
Journal:  Microb Ecol       Date:  2013-04-28       Impact factor: 4.552

4.  Functional investigation of two 1-aminocyclopropane-1-carboxylate (ACC) synthase-like genes in the moss Physcomitrella patens.

Authors:  Lifang Sun; Hui Dong; Yuanyuan Mei; Ning Ning Wang
Journal:  Plant Cell Rep       Date:  2016-01-08       Impact factor: 4.570

Review 5.  Biologically inspired intelligent decision making: a commentary on the use of artificial neural networks in bioinformatics.

Authors:  Timmy Manning; Roy D Sleator; Paul Walsh
Journal:  Bioengineered       Date:  2013-12-16       Impact factor: 3.269

6.  Genetics just got SEXY: Sequences encoding XY.

Authors:  Roy D Sleator
Journal:  Bioengineered       Date:  2014-05-21       Impact factor: 3.269

7.  Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes.

Authors:  Manoj Kumar Verma; Vasim Ahmed; Shashank Gupta; Jitendra Kumar; Rajesh Pandey; Vibha Mandhan; Nar Singh Chauhan
Journal:  Sci Rep       Date:  2018-01-23       Impact factor: 4.379

8.  Digital biology: a new era has begun.

Authors:  Roy D Sleator
Journal:  Bioengineered       Date:  2012 Nov-Dec       Impact factor: 3.269

9.  Analysis of the role of the Cronobacter sakazakii ProP homologues in osmotolerance.

Authors:  Audrey Feeney; Christopher D Johnston; Rodney Govender; Jim O'Mahony; Aidan Coffey; Roy D Sleator
Journal:  Gut Pathog       Date:  2014-05-24       Impact factor: 4.181

10.  Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15'-monooxygenase.

Authors:  Eamonn P Culligan; Roy D Sleator; Julian R Marchesi; Colin Hill
Journal:  PLoS One       Date:  2014-07-24       Impact factor: 3.240

  10 in total

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