Literature DB >> 26658741

Reads meet rotamers: structural biology in the age of deep sequencing.

Anurag Sethi1, Declan Clarke2, Jieming Chen3, Sushant Kumar1, Timur R Galeev1, Lynne Regan4, Mark Gerstein5.   

Abstract

Structure has traditionally been interrelated with sequence, usually in the framework of comparing sequences across species sharing a common fold. However, the nature of information within the sequence and structure databases is evolving, changing the type of comparisons possible. In particular, we now have a vast amount of personal genome sequences from human populations and a greater fraction of new structures contain interacting proteins within large complexes. Consequently, we have to recast our conception of sequence conservation and its relation to structure-for example, focusing more on selection within the human population. Moreover, within structural biology there is less emphasis on the discovery of novel folds and more on relating structures to networks of protein interactions. We cover this changing mindset here.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 26658741      PMCID: PMC4751031          DOI: 10.1016/j.sbi.2015.11.003

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


  62 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The human disease network.

Authors:  Kwang-Il Goh; Michael E Cusick; David Valle; Barton Childs; Marc Vidal; Albert-László Barabási
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-14       Impact factor: 11.205

Review 3.  The role of regulatory variation in complex traits and disease.

Authors:  Frank W Albert; Leonid Kruglyak
Journal:  Nat Rev Genet       Date:  2015-02-24       Impact factor: 53.242

Review 4.  Disease mutations in disordered regions--exception to the rule?

Authors:  Vladimir Vacic; Lilia M Iakoucheva
Journal:  Mol Biosyst       Date:  2011-11-14

Review 5.  Biophysical characterization of intrinsically disordered proteins.

Authors:  David Eliezer
Journal:  Curr Opin Struct Biol       Date:  2009-01-21       Impact factor: 6.809

6.  Evolution of oligomeric state through allosteric pathways that mimic ligand binding.

Authors:  Tina Perica; Yasushi Kondo; Sandhya P Tiwari; Stephen H McLaughlin; Katherine R Kemplen; Xiuwei Zhang; Annette Steward; Nathalie Reuter; Jane Clarke; Sarah A Teichmann
Journal:  Science       Date:  2014-12-19       Impact factor: 47.728

7.  A global reference for human genetic variation.

Authors:  Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis
Journal:  Nature       Date:  2015-10-01       Impact factor: 49.962

8.  The Human Gene Mutation Database: 2008 update.

Authors:  Peter D Stenson; Matthew Mort; Edward V Ball; Katy Howells; Andrew D Phillips; Nick St Thomas; David N Cooper
Journal:  Genome Med       Date:  2009-01-22       Impact factor: 11.117

9.  SNAP: predict effect of non-synonymous polymorphisms on function.

Authors:  Yana Bromberg; Burkhard Rost
Journal:  Nucleic Acids Res       Date:  2007-05-25       Impact factor: 16.971

10.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

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  3 in total

1.  Intensification: A Resource for Amplifying Population-Genetic Signals with Protein Repeats.

Authors:  Jieming Chen; Bo Wang; Lynne Regan; Mark Gerstein
Journal:  J Mol Biol       Date:  2016-12-07       Impact factor: 5.469

2.  Localized structural frustration for evaluating the impact of sequence variants.

Authors:  Sushant Kumar; Declan Clarke; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2016-10-18       Impact factor: 16.971

3.  Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation.

Authors:  Declan Clarke; Anurag Sethi; Shantao Li; Sushant Kumar; Richard W F Chang; Jieming Chen; Mark Gerstein
Journal:  Structure       Date:  2016-04-07       Impact factor: 5.006

  3 in total

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