Literature DB >> 33104802

SMART: recent updates, new developments and status in 2020.

Ivica Letunic1, Supriya Khedkar2, Peer Bork2,3,4.   

Abstract

SMART (Simple Modular Architecture Research Tool) is a web resource (https://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 9 contains manually curated models for more than 1300 protein domains, with a topical set of 68 new models added since our last update article (1). All the new models are for diverse recombinase families and subfamilies and as a set they provide a comprehensive overview of mobile element recombinases namely transposase, integrase, relaxase, resolvase, cas1 casposase and Xer like cellular recombinase. Further updates include the synchronization of the underlying protein databases with UniProt (2), Ensembl (3) and STRING (4), greatly increasing the total number of annotated domains and other protein features available in architecture analysis mode. Furthermore, SMART's vector-based protein display engine has been extended and updated to use the latest web technologies and the domain architecture analysis components have been optimized to handle the increased number of protein features available.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID: 33104802      PMCID: PMC7778883          DOI: 10.1093/nar/gkaa937

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  15 in total

1.  SMART, a simple modular architecture research tool: identification of signaling domains.

Authors:  J Schultz; F Milpetz; P Bork; C P Ponting
Journal:  Proc Natl Acad Sci U S A       Date:  1998-05-26       Impact factor: 11.205

Review 2.  NCBI Taxonomy: a comprehensive update on curation, resources and tools.

Authors:  Conrad L Schoch; Stacy Ciufo; Mikhail Domrachev; Carol L Hotton; Sivakumar Kannan; Rogneda Khovanskaya; Detlef Leipe; Richard Mcveigh; Kathleen O'Neill; Barbara Robbertse; Shobha Sharma; Vladimir Soussov; John P Sullivan; Lu Sun; Seán Turner; Ilene Karsch-Mizrachi
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

Review 3.  Mechanisms of DNA Transposition.

Authors:  Alison B Hickman; Fred Dyda
Journal:  Microbiol Spectr       Date:  2015-04

4.  Hidden Markov models in computational biology. Applications to protein modeling.

Authors:  A Krogh; M Brown; I S Mian; K Sjölander; D Haussler
Journal:  J Mol Biol       Date:  1994-02-04       Impact factor: 5.469

5.  Accelerated Profile HMM Searches.

Authors:  Sean R Eddy
Journal:  PLoS Comput Biol       Date:  2011-10-20       Impact factor: 4.475

6.  20 years of the SMART protein domain annotation resource.

Authors:  Ivica Letunic; Peer Bork
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

7.  STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.

Authors:  Damian Szklarczyk; Annika L Gable; David Lyon; Alexander Junge; Stefan Wyder; Jaime Huerta-Cepas; Milan Simonovic; Nadezhda T Doncheva; John H Morris; Peer Bork; Lars J Jensen; Christian von Mering
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

8.  Ensembl 2020.

Authors:  Andrew D Yates; Premanand Achuthan; Wasiu Akanni; James Allen; Jamie Allen; Jorge Alvarez-Jarreta; M Ridwan Amode; Irina M Armean; Andrey G Azov; Ruth Bennett; Jyothish Bhai; Konstantinos Billis; Sanjay Boddu; José Carlos Marugán; Carla Cummins; Claire Davidson; Kamalkumar Dodiya; Reham Fatima; Astrid Gall; Carlos Garcia Giron; Laurent Gil; Tiago Grego; Leanne Haggerty; Erin Haskell; Thibaut Hourlier; Osagie G Izuogu; Sophie H Janacek; Thomas Juettemann; Mike Kay; Ilias Lavidas; Tuan Le; Diana Lemos; Jose Gonzalez Martinez; Thomas Maurel; Mark McDowall; Aoife McMahon; Shamika Mohanan; Benjamin Moore; Michael Nuhn; Denye N Oheh; Anne Parker; Andrew Parton; Mateus Patricio; Manoj Pandian Sakthivel; Ahamed Imran Abdul Salam; Bianca M Schmitt; Helen Schuilenburg; Dan Sheppard; Mira Sycheva; Marek Szuba; Kieron Taylor; Anja Thormann; Glen Threadgold; Alessandro Vullo; Brandon Walts; Andrea Winterbottom; Amonida Zadissa; Marc Chakiachvili; Bethany Flint; Adam Frankish; Sarah E Hunt; Garth IIsley; Myrto Kostadima; Nick Langridge; Jane E Loveland; Fergal J Martin; Joannella Morales; Jonathan M Mudge; Matthieu Muffato; Emily Perry; Magali Ruffier; Stephen J Trevanion; Fiona Cunningham; Kevin L Howe; Daniel R Zerbino; Paul Flicek
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

9.  CD-HIT: accelerated for clustering the next-generation sequencing data.

Authors:  Limin Fu; Beifang Niu; Zhengwei Zhu; Sitao Wu; Weizhong Li
Journal:  Bioinformatics       Date:  2012-10-11       Impact factor: 6.937

10.  Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity.

Authors:  Mart Krupovic; Kira S Makarova; Patrick Forterre; David Prangishvili; Eugene V Koonin
Journal:  BMC Biol       Date:  2014-05-19       Impact factor: 7.431

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  195 in total

1.  A putative effector of the rubber-tree powdery mildew fungus has elicitor activity that can trigger plant immunity.

Authors:  Xiao Li; Mengyao Liu; Yuhan Liu; Wenyuan Zhao; Sipeng Li; Wenbo Liu; Chunhua Lin; Weiguo Miao
Journal:  Planta       Date:  2022-01-07       Impact factor: 4.116

2.  Deduction and exploration of the evolution and function of vertebrate GFPT family.

Authors:  Si-Ang Wei; Ran Xu; Yu-Yao Ji; Zhi-Wen Ding; Yun-Zeng Zou
Journal:  Genes Genomics       Date:  2022-01-17       Impact factor: 1.839

Review 3.  The role of junctophilin proteins in cellular function.

Authors:  Stephan E Lehnart; Xander H T Wehrens
Journal:  Physiol Rev       Date:  2022-01-10       Impact factor: 37.312

4.  Identification and analysis of iron transporters from the fission yeast Schizosaccharomyces pombe.

Authors:  Fawad Ahmad; Ying Luo; Helong Yin; Yun Zhang; Ying Huang
Journal:  Arch Microbiol       Date:  2022-01-26       Impact factor: 2.552

Review 5.  Co-Transcriptional RNA Processing in Plants: Exploring from the Perspective of Polyadenylation.

Authors:  Jing Yang; Ying Cao; Ligeng Ma
Journal:  Int J Mol Sci       Date:  2021-03-24       Impact factor: 5.923

Review 6.  Composition and function of ciliary inner-dynein-arm subunits studied in Chlamydomonas reinhardtii.

Authors:  Ryosuke Yamamoto; Juyeon Hwang; Takashi Ishikawa; Takahide Kon; Winfield S Sale
Journal:  Cytoskeleton (Hoboken)       Date:  2021-04-28

7.  Hybrid Histidine Kinase BinK Represses Vibrio fischeri Biofilm Signaling at Multiple Developmental Stages.

Authors:  Denise A Ludvik; Katherine M Bultman; Mark J Mandel
Journal:  J Bacteriol       Date:  2021-07-08       Impact factor: 3.490

8.  KCTD19 and its associated protein ZFP541 are independently essential for meiosis in male mice.

Authors:  Seiya Oura; Takayuki Koyano; Chisato Kodera; Yuki Horisawa-Takada; Makoto Matsuyama; Kei-Ichiro Ishiguro; Masahito Ikawa
Journal:  PLoS Genet       Date:  2021-05-07       Impact factor: 5.917

9.  Diversification of the calponin family proteins by gene amplification and repeat expansion of calponin-like motifs.

Authors:  Shoichiro Ono
Journal:  Cytoskeleton (Hoboken)       Date:  2021-08-18

10.  Regulation of the Phosphoinositide Code by Phosphorylation of Membrane Readers.

Authors:  Troy A Kervin; Michael Overduin
Journal:  Cells       Date:  2021-05-14       Impact factor: 6.600

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