Literature DB >> 33095862

ThermoMutDB: a thermodynamic database for missense mutations.

Joicymara S Xavier1,2, Thanh-Binh Nguyen3, Malancha Karmarkar3,4, Stephanie Portelli3,4, Pâmela M Rezende2, João P L Velloso2, David B Ascher3,4,5, Douglas E V Pires3,4,6.   

Abstract

Proteins are intricate, dynamic structures, and small changes in their amino acid sequences can lead to large effects on their folding, stability and dynamics. To facilitate the further development and evaluation of methods to predict these changes, we have developed ThermoMutDB, a manually curated database containing >14,669 experimental data of thermodynamic parameters for wild type and mutant proteins. This represents an increase of 83% in unique mutations over previous databases and includes thermodynamic information on 204 new proteins. During manual curation we have also corrected annotation errors in previously curated entries. Associated with each entry, we have included information on the unfolding Gibbs free energy and melting temperature change, and have associated entries with available experimental structural information. ThermoMutDB supports users to contribute to new data points and programmatic access to the database via a RESTful API. ThermoMutDB is freely available at: http://biosig.unimelb.edu.au/thermomutdb.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID: 33095862      PMCID: PMC7778973          DOI: 10.1093/nar/gkaa925

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


  34 in total

1.  Residue depth: a novel parameter for the analysis of protein structure and stability.

Authors:  S Chakravarty; R Varadarajan
Journal:  Structure       Date:  1999-07-15       Impact factor: 5.006

2.  MAESTROweb: a web server for structure-based protein stability prediction.

Authors:  Josef Laimer; Julia Hiebl-Flach; Daniel Lengauer; Peter Lackner
Journal:  Bioinformatics       Date:  2016-01-06       Impact factor: 6.937

3.  Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma.

Authors:  Mariam Jafri; Naomi C Wake; David B Ascher; Douglas E V Pires; Dean Gentle; Mark R Morris; Eleanor Rattenberry; Michael A Simpson; Richard C Trembath; Astrid Weber; Emma R Woodward; Alan Donaldson; Tom L Blundell; Farida Latif; Eamonn R Maher
Journal:  Cancer Discov       Date:  2015-04-14       Impact factor: 39.397

Review 4.  Structure- and sequence-analysis inspired engineering of proteins for enhanced thermostability.

Authors:  Hein J Wijma; Robert J Floor; Dick B Janssen
Journal:  Curr Opin Struct Biol       Date:  2013-05-15       Impact factor: 6.809

5.  Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource.

Authors:  Stephanie Portelli; Moshe Olshansky; Carlos H M Rodrigues; Elston N D'Souza; Yoochan Myung; Michael Silk; Azadeh Alavi; Douglas E V Pires; David B Ascher
Journal:  Nat Genet       Date:  2020-10       Impact factor: 38.330

6.  Huntingtin Inclusions Trigger Cellular Quiescence, Deactivate Apoptosis, and Lead to Delayed Necrosis.

Authors:  Yasmin M Ramdzan; Mikhail M Trubetskov; Angelique R Ormsby; Estella A Newcombe; Xiaojing Sui; Mark J Tobin; Marie N Bongiovanni; Sally L Gras; Grant Dewson; Jason M L Miller; Steven Finkbeiner; Nagaraj S Moily; Jonathan Niclis; Clare L Parish; Anthony W Purcell; Michael J Baker; Jacqueline A Wilce; Saboora Waris; Diana Stojanovski; Till Böcking; Ching-Seng Ang; David B Ascher; Gavin E Reid; Danny M Hatters
Journal:  Cell Rep       Date:  2017-05-02       Impact factor: 9.423

Review 7.  Genomes, structural biology and drug discovery: combating the impacts of mutations in genetic disease and antibiotic resistance.

Authors:  Arun Prasad Pandurangan; David B Ascher; Sherine E Thomas; Tom L Blundell
Journal:  Biochem Soc Trans       Date:  2017-04-15       Impact factor: 5.407

8.  PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality.

Authors:  Yang Yang; Siddhaling Urolagin; Abhishek Niroula; Xuesong Ding; Bairong Shen; Mauno Vihinen
Journal:  Int J Mol Sci       Date:  2018-03-28       Impact factor: 5.923

9.  Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis.

Authors:  Stephanie Portelli; Jody E Phelan; David B Ascher; Taane G Clark; Nicholas Furnham
Journal:  Sci Rep       Date:  2018-10-18       Impact factor: 4.379

10.  A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction.

Authors:  Joanne M Hildebrand; Maria Kauppi; Ian J Majewski; Zikou Liu; Allison J Cox; Sanae Miyake; Emma J Petrie; Michael A Silk; Zhixiu Li; Maria C Tanzer; Gabriela Brumatti; Samuel N Young; Cathrine Hall; Sarah E Garnish; Jason Corbin; Michael D Stutz; Ladina Di Rago; Pradnya Gangatirkar; Emma C Josefsson; Kristin Rigbye; Holly Anderton; James A Rickard; Anne Tripaydonis; Julie Sheridan; Thomas S Scerri; Victoria E Jackson; Peter E Czabotar; Jian-Guo Zhang; Leila Varghese; Cody C Allison; Marc Pellegrini; Gillian M Tannahill; Esme C Hatchell; Tracy A Willson; Dina Stockwell; Carolyn A de Graaf; Janelle Collinge; Adrienne Hilton; Natasha Silke; Sukhdeep K Spall; Diep Chau; Vicki Athanasopoulos; Donald Metcalf; Ronald M Laxer; Alexander G Bassuk; Benjamin W Darbro; Maria A Fiatarone Singh; Nicole Vlahovich; David Hughes; Maria Kozlovskaia; David B Ascher; Klaus Warnatz; Nils Venhoff; Jens Thiel; Christine Biben; Stefan Blum; John Reveille; Michael S Hildebrand; Carola G Vinuesa; Pamela McCombe; Matthew A Brown; Benjamin T Kile; Catriona McLean; Melanie Bahlo; Seth L Masters; Hiroyasu Nakano; Polly J Ferguson; James M Murphy; Warren S Alexander; John Silke
Journal:  Nat Commun       Date:  2020-06-19       Impact factor: 14.919

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  8 in total

1.  Turning Failures into Applications: The Problem of Protein ΔΔG Prediction.

Authors:  Rita Casadio; Castrense Savojardo; Piero Fariselli; Emidio Capriotti; Pier Luigi Martelli
Journal:  Methods Mol Biol       Date:  2022

2.  Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset.

Authors:  Corrado Pancotti; Silvia Benevenuta; Giovanni Birolo; Virginia Alberini; Valeria Repetto; Tiziana Sanavia; Emidio Capriotti; Piero Fariselli
Journal:  Brief Bioinform       Date:  2022-03-10       Impact factor: 11.622

Review 3.  Ecosystem-specific microbiota and microbiome databases in the era of big data.

Authors:  Victor Lobanov; Angélique Gobet; Alyssa Joyce
Journal:  Environ Microbiome       Date:  2022-07-16

4.  Protposer: The web server that readily proposes protein stabilizing mutations with high PPV.

Authors:  Helena García-Cebollada; Alfonso López; Javier Sancho
Journal:  Comput Struct Biotechnol J       Date:  2022-05-10       Impact factor: 6.155

5.  The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.

Authors:  Daniel J Rigden; Xosé M Fernández
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

6.  Investigation of changes in protein stability and substrate affinity of 3CL-protease of SARS-CoV-2 caused by mutations.

Authors:  Ekrem Akbulut
Journal:  Genet Mol Biol       Date:  2022-04-29       Impact factor: 2.087

7.  Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures.

Authors:  Qisheng Pan; Thanh Binh Nguyen; David B Ascher; Douglas E V Pires
Journal:  Brief Bioinform       Date:  2022-03-10       Impact factor: 13.994

Review 8.  Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures.

Authors:  Benjamin B V Louis; Luciano A Abriata
Journal:  Mol Biotechnol       Date:  2021-06-08       Impact factor: 2.695

  8 in total

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