Literature DB >> 26451980

The language of the protein universe.

Andrea Scaiewicz1, Michael Levitt2.   

Abstract

Proteins, the main cell machinery which play a major role in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the 'Rosetta Stone' of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Entities:  

Mesh:

Substances:

Year:  2015        PMID: 26451980      PMCID: PMC4695241          DOI: 10.1016/j.gde.2015.08.010

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  71 in total

1.  SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments.

Authors:  Julian Gough; Cyrus Chothia
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

Review 2.  The language of genes.

Authors:  David B Searls
Journal:  Nature       Date:  2002-11-14       Impact factor: 49.962

3.  CDART: protein homology by domain architecture.

Authors:  Lewis Y Geer; Michael Domrachev; David J Lipman; Stephen H Bryant
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

4.  Classification of proteins: available structural space for molecular modeling.

Authors:  Antonina Andreeva
Journal:  Methods Mol Biol       Date:  2012

5.  Domain rearrangements in protein evolution.

Authors:  Asa K Björklund; Diana Ekman; Sara Light; Johannes Frey-Skött; Arne Elofsson
Journal:  J Mol Biol       Date:  2005-09-21       Impact factor: 5.469

6.  DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins.

Authors:  Andrew D Moore; Andreas Held; Nicolas Terrapon; January Weiner; Erich Bornberg-Bauer
Journal:  Bioinformatics       Date:  2013-11-12       Impact factor: 6.937

7.  A decade after the first full human genome sequencing: when will we understand our own genome?

Authors:  Frank Eisenhaber
Journal:  J Bioinform Comput Biol       Date:  2012-06-22       Impact factor: 1.122

8.  MoonProt: a database for proteins that are known to moonlight.

Authors:  Mathew Mani; Chang Chen; Vaishak Amblee; Haipeng Liu; Tanu Mathur; Grant Zwicke; Shadi Zabad; Bansi Patel; Jagravi Thakkar; Constance J Jeffery
Journal:  Nucleic Acids Res       Date:  2014-10-16       Impact factor: 16.971

9.  ECOD: an evolutionary classification of protein domains.

Authors:  Hua Cheng; R Dustin Schaeffer; Yuxing Liao; Lisa N Kinch; Jimin Pei; Shuoyong Shi; Bong-Hyun Kim; Nick V Grishin
Journal:  PLoS Comput Biol       Date:  2014-12-04       Impact factor: 4.475

10.  Global patterns of protein domain gain and loss in superkingdoms.

Authors:  Arshan Nasir; Kyung Mo Kim; Gustavo Caetano-Anollés
Journal:  PLoS Comput Biol       Date:  2014-01-30       Impact factor: 4.475

View more
  11 in total

1.  Targeted insertional mutagenesis libraries for deep domain insertion profiling.

Authors:  Willow Coyote-Maestas; David Nedrud; Steffan Okorafor; Yungui He; Daniel Schmidt
Journal:  Nucleic Acids Res       Date:  2020-01-24       Impact factor: 16.971

2.  BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models.

Authors:  Hong-Liang Li; Yi-He Pang; Bin Liu
Journal:  Nucleic Acids Res       Date:  2021-12-16       Impact factor: 16.971

3.  Exploring the dark foldable proteome by considering hydrophobic amino acids topology.

Authors:  Tristan Bitard-Feildel; Isabelle Callebaut
Journal:  Sci Rep       Date:  2017-01-30       Impact factor: 4.379

4.  Hemoglobin state-flux: A finite-state model representation of the hemoglobin signal for evaluation of the resting state and the influence of disease.

Authors:  Randall L Barbour; Harry L Graber; San-Lian S Barbour
Journal:  PLoS One       Date:  2018-06-08       Impact factor: 3.240

5.  Secreted Cysteine-Rich Repeat Proteins "SCREPs": A Novel Multi-Domain Architecture.

Authors:  Michael Maxwell; Eivind A B Undheim; Mehdi Mobli
Journal:  Front Pharmacol       Date:  2018-11-20       Impact factor: 5.810

6.  Grammar of protein domain architectures.

Authors:  Lijia Yu; Deepak Kumar Tanwar; Emanuel Diego S Penha; Yuri I Wolf; Eugene V Koonin; Malay Kumar Basu
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-07       Impact factor: 11.205

7.  Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling.

Authors:  Willow Coyote-Maestas; David Nedrud; Antonio Suma; Yungui He; Kenneth A Matreyek; Douglas M Fowler; Vincenzo Carnevale; Chad L Myers; Daniel Schmidt
Journal:  Nat Commun       Date:  2021-12-08       Impact factor: 14.919

Review 8.  Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.

Authors:  Antonina Andreeva
Journal:  Biochem Soc Trans       Date:  2016-06-15       Impact factor: 5.407

9.  Unique function words characterize genomic proteins.

Authors:  Andrea Scaiewicz; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2018-06-12       Impact factor: 11.205

Review 10.  Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences.

Authors:  Tristan Bitard-Feildel; Alexis Lamiable; Jean-Paul Mornon; Isabelle Callebaut
Journal:  Proteomics       Date:  2018-10-30       Impact factor: 3.984

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.