Literature DB >> 28150231

Protein Bioinformatics Databases and Resources.

Chuming Chen1, Hongzhan Huang2, Cathy H Wu3,4.   

Abstract

Many publicly available data repositories and resources have been developed to support protein-related information management, data-driven hypothesis generation, and biological knowledge discovery. To help researchers quickly find the appropriate protein-related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.

Entities:  

Keywords:  Big data; Bioinformatics; Data analytics; Data integration; Database; PTM; Pathway; Protein family; Protein function; Protein interaction; Protein mutation; Protein sequence; Protein structure; Proteomics

Mesh：

Substances：

Year:  2017        PMID： 28150231      PMCID： PMC5506686          DOI： 10.1007/978-1-4939-6783-4_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  178 in total

1.  Announcing the worldwide Protein Data Bank.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura
Journal:  Nat Struct Biol       Date:  2003-12

2.  SWISS-2DPAGE, ten years later.

Authors:  Christine Hoogland; Khaled Mostaguir; Jean-Charles Sanchez; Denis F Hochstrasser; Ron D Appel
Journal:  Proteomics       Date:  2004-08       Impact factor: 3.984

3.  A family of evolution-entropy hybrid methods for ranking protein residues by importance.

Authors:  I Mihalek; I Res; O Lichtarge
Journal:  J Mol Biol       Date:  2004-03-05       Impact factor: 5.469

4.  DMDM: domain mapping of disease mutations.

Authors:  Thomas A Peterson; Asa Adadey; Ivette Santana-Cruz; Yanan Sun; Andrew Winder; Maricel G Kann
Journal:  Bioinformatics       Date:  2010-08-04       Impact factor: 6.937

5.  Bio2RDF: towards a mashup to build bioinformatics knowledge systems.

Authors:  François Belleau; Marc-Alexandre Nolin; Nicole Tourigny; Philippe Rigault; Jean Morissette
Journal:  J Biomed Inform       Date:  2008-03-21       Impact factor: 6.317

6.  Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis.

Authors:  Stephane Decramer; Stefan Wittke; Harald Mischak; Petra Zürbig; Michael Walden; François Bouissou; Jean-Loup Bascands; Joost P Schanstra
Journal:  Nat Med       Date:  2006-03-19       Impact factor: 53.440

7.  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.

Authors:  Baris E Suzek; Yuqi Wang; Hongzhan Huang; Peter B McGarvey; Cathy H Wu
Journal:  Bioinformatics       Date:  2014-11-13       Impact factor: 6.937

8.  H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.

Authors:  Chisato Yamasaki; Katsuhiko Murakami; Jun-ichi Takeda; Yoshiharu Sato; Akiko Noda; Ryuichi Sakate; Takuya Habara; Hajime Nakaoka; Fusano Todokoro; Akihiro Matsuya; Tadashi Imanishi; Takashi Gojobori
Journal:  Nucleic Acids Res       Date:  2009-11-23       Impact factor: 16.971

9.  Proteome-based plasma biomarkers for Alzheimer's disease.

Authors:  A Hye; S Lynham; M Thambisetty; M Causevic; J Campbell; H L Byers; C Hooper; F Rijsdijk; S J Tabrizi; S Banner; C E Shaw; C Foy; M Poppe; N Archer; G Hamilton; J Powell; R G Brown; P Sham; M Ward; S Lovestone
Journal:  Brain       Date:  2006-11       Impact factor: 13.501

10.  Gramene 2013: comparative plant genomics resources.

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Journal:  Nucleic Acids Res       Date:  2013-11-11       Impact factor: 16.971
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  49 in total

1.  Benzo[ a]pyrene Induction of Glutathione S-Transferases: An Activity-Based Protein Profiling Investigation.

Authors:  Ethan G Stoddard; Bryan J Killinger; Subhasree A Nag; Jude Martin; Richard Corley; Jordan N Smith; Aaron T Wright
Journal:  Chem Res Toxicol       Date:  2019-04-12       Impact factor: 3.739

2.  SeQuery: an interactive graph database for visualizing the GPCR superfamily.

Authors:  Geng-Ming Hu; M K Secario; Chi-Ming Chen
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

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Authors:  Adeniyi T Adewumi; Pritika Ramharack; Opeyemi S Soremekun; Mahmoud E S Soliman
Journal:  Protein J       Date:  2020-04       Impact factor: 2.371

4.  On the control of the proton current in the voltage-gated proton channel Hv1.

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Journal:  Proc Natl Acad Sci U S A       Date:  2018-09-25       Impact factor: 11.205

5.  Enzymatic reconstitution of ribosomal peptide backbone thioamidation.

Authors:  Nilkamal Mahanta; Andi Liu; Shihui Dong; Satish K Nair; Douglas A Mitchell
Journal:  Proc Natl Acad Sci U S A       Date:  2018-03-05       Impact factor: 11.205

6.  Bioinformatics Structural and Phylogenetic Characterization of Entamoeba histolytica Alcohol Dehydrogenase 2 (EhADH2).

Authors:  Katie M Lowerre; Avelina Espinosa; Guillermo Paz-Y-Miño-C; Christopher Hemme
Journal:  Bios       Date:  2019-10-26

7.  An in silico proteomics screen to predict and prioritize protein-protein interactions dependent on post-translationally modified motifs.

Authors:  Anna M Schmoker; Heather E Driscoll; Stefanie R Geiger; James J Vincent; Alicia M Ebert; Bryan A Ballif
Journal:  Bioinformatics       Date:  2018-11-15       Impact factor: 6.937

8.  Exposure to an Environmental Mixture of Polycyclic Aromatic Hydrocarbons Induces Hepatic Cytochrome P450 Enzymes in Mice.

Authors:  Ethan G Stoddard; Subhasree Nag; Jude Martin; Kimberly J Tyrrell; Teresa Gibbins; Kim A Anderson; Anil K Shukla; Richard Corley; Aaron T Wright; Jordan N Smith
Journal:  Chem Res Toxicol       Date:  2021-09-02       Impact factor: 3.973

9.  Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias.

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Journal:  BMC Genomics       Date:  2021-07-21       Impact factor: 3.969

10.  In vitro and in silico analysis reveals antifungal activity and potential targets of curcumin on Paracoccidioides spp.

Authors:  Olívia Basso Rocha; Lívia do Carmo Silva; Marcos Antonio Batista de Carvalho Júnior; Amanda Alves de Oliveira; Célia Maria de Almeida Soares; Maristela Pereira
Journal:  Braz J Microbiol       Date:  2021-07-29       Impact factor: 2.214
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