Literature DB >> 22884875

Current challenges in genome annotation through structural biology and bioinformatics.

Nicholas Furnham1, Tjaart A P de Beer, Janet M Thornton.   

Abstract

With the huge volume in genomic sequences being generated from high-throughout sequencing projects the requirement for providing accurate and detailed annotations of gene products has never been greater. It is proving to be a huge challenge for computational biologists to use as much information as possible from experimental data to provide annotations for genome data of unknown function. A central component to this process is to use experimentally determined structures, which provide a means to detect homology that is not discernable from just the sequence and permit the consequences of genomic variation to be realized at the molecular level. In particular, structures also form the basis of many bioinformatics methods for improving the detailed functional annotations of enzymes in combination with similarities in sequence and chemistry.
Copyright © 2012. Published by Elsevier Ltd.

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Year:  2012        PMID: 22884875     DOI: 10.1016/j.sbi.2012.07.005

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  6 in total

Review 1.  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

2.  Types and effects of protein variations.

Authors:  Mauno Vihinen
Journal:  Hum Genet       Date:  2015-01-24       Impact factor: 4.132

3.  Model-driven discovery of underground metabolic functions in Escherichia coli.

Authors:  Gabriela I Guzmán; José Utrilla; Sergey Nurk; Elizabeth Brunk; Jonathan M Monk; Ali Ebrahim; Bernhard O Palsson; Adam M Feist
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-06       Impact factor: 11.205

4.  A Collaborative Classroom Investigation of the Evolution of SABATH Methyltransferase Substrate Preference Shifts over 120 My of Flowering Plant History.

Authors:  Nicole M Dubs; Breck R Davis; Victor de Brito; Kate C Colebrook; Ian J Tiefel; Madison B Nakayama; Ruiqi Huang; Audrey E Ledvina; Samantha J Hack; Brent Inkelaar; Talline R Martins; Sarah M Aartila; Kelli S Albritton; Sarah Almuhanna; Ryan J Arnoldi; Clara K Austin; Amber C Battle; Gregory R Begeman; Caitlin M Bickings; Jonathon T Bradfield; Eric C Branch; Eric P Conti; Breana Cooley; Nicole M Dotson; Cheyone J Evans; Amber S Fries; Ivan G Gilbert; Weston D Hillier; Pornkamol Huang; Kaitlin W Hyde; Filip Jevtovic; Mark C Johnson; Julie L Keeler; Albert Lam; Kyle M Leach; Jeremy D Livsey; Jonathan T Lo; Kevin R Loney; Nich W Martin; Amber S Mazahem; Aurora N Mokris; Destiny M Nichols; Ruchi Ojha; Nnanna N Okorafor; Joshua R Paris; Thais Fuscaldi Reboucas; Pedro Beretta Sant'Anna; Mathew R Seitz; Nathan R Seymour; Lila K Slaski; Stephen O Stemaly; Benjamin R Ulrich; Emile N Van Meter; Meghan L Young; Todd J Barkman
Journal:  Mol Biol Evol       Date:  2022-03-02       Impact factor: 16.240

Review 5.  Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence.

Authors:  José T Moreira-Filho; Arthur C Silva; Rafael F Dantas; Barbara F Gomes; Lauro R Souza Neto; Jose Brandao-Neto; Raymond J Owens; Nicholas Furnham; Bruno J Neves; Floriano P Silva-Junior; Carolina H Andrade
Journal:  Front Immunol       Date:  2021-05-31       Impact factor: 7.561

6.  No one tool to rule them all: Prokaryotic gene prediction tool annotations are highly dependent on the organism of study.

Authors:  Nicholas J Dimonaco; Wayne Aubrey; Kim Kenobi; Amanda Clare; Christopher J Creevey
Journal:  Bioinformatics       Date:  2021-12-07       Impact factor: 6.937

  6 in total

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