Treffer: ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years.

Title:
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years.
Authors:
Nikam R; Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India., Kulandaisamy A; Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India., Harini K; Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India., Sharma D; Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India., Gromiha MM; Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India.
Source:
Nucleic acids research [Nucleic Acids Res] 2021 Jan 08; Vol. 49 (D1), pp. D420-D424.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
Imprint Name(s):
Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
MeSH Terms:
Databases, Protein*, Mutant Proteins/*chemistry , Proteins/*chemistry, Information Storage and Retrieval ; Statistics as Topic ; Thermodynamics
References:
Biopolymers. 2001-2002;61(2):121-6. (PMID: 11987161)
J Mol Biol. 2021 May 28;433(11):166646. (PMID: 32920050)
Arch Med Res. 2006 Aug;37(6):696-9. (PMID: 16824927)
Sci Rep. 2016 Mar 18;6:23257. (PMID: 26988870)
Structure. 2007 Dec;15(12):1567-76. (PMID: 18073107)
J Mol Biol. 2013 Nov 1;425(21):3919-36. (PMID: 23871686)
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515. (PMID: 30395287)
J Protein Chem. 1999 Jul;18(5):565-78. (PMID: 10524774)
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D120-1. (PMID: 14681373)
Brief Bioinform. 2021 Mar 22;22(2):2119-2125. (PMID: 32337573)
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W239-42. (PMID: 16845001)
Proteins. 2006 Mar 1;62(4):1125-32. (PMID: 16372356)
Nucleic Acids Res. 2002 Jan 1;30(1):301-2. (PMID: 11752320)
Adv Bioinformatics. 2014;2014:278385. (PMID: 25197272)
Nucleic Acids Res. 1999 Jan 1;27(1):286-8. (PMID: 9847203)
Nucleic Acids Res. 2018 Jul 2;46(W1):W350-W355. (PMID: 29718330)
Biopolymers. 2006 May;82(1):80-92. (PMID: 16453276)
J Theor Biol. 1994 Aug 21;169(4):419-32. (PMID: 7526075)
BMC Bioinformatics. 2019 Jul 3;20(Suppl 14):335. (PMID: 31266447)
Protein Eng Des Sel. 2008 Jan;21(1):37-44. (PMID: 18096555)
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D204-6. (PMID: 16381846)
PLoS One. 2014 Oct 23;9(10):e110439. (PMID: 25340340)
Science. 2014 Oct 3;346(6205):1255784. (PMID: 25278616)
J Proteome Res. 2016 Dec 2;15(12):4666-4674. (PMID: 27794609)
Biochemistry. 1999 Jan 26;38(4):1377-85. (PMID: 9931001)
J Mol Biol. 2017 Apr 7;429(7):948-963. (PMID: 27964946)
Methods Mol Biol. 2017;1607:627-641. (PMID: 28573592)
Int J Mol Sci. 2018 Mar 28;19(4):. (PMID: 29597263)
Biopolymers. 1983 Dec;22(12):2577-637. (PMID: 6667333)
Nucleic Acids Res. 2019 Jan 8;47(D1):D482-D489. (PMID: 30445541)
BMC Genomics. 2016 Jun 23;17 Suppl 2:397. (PMID: 27356511)
BMC Bioinformatics. 2011 May 13;12:151. (PMID: 21569468)
J Mol Biol. 2016 Mar 27;428(6):1394-1405. (PMID: 26804571)
BMC Bioinformatics. 2015 Apr 16;16:116. (PMID: 25885774)
Bioinformatics. 2014 Feb 01;30(3):335-42. (PMID: 24281696)
Biochemistry. 2000 Mar 28;39(12):3480-5. (PMID: 10727243)
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W306-10. (PMID: 15980478)
Hum Mutat. 2011 Oct;32(10):1161-70. (PMID: 21853506)
Substance Nomenclature:
0 (Mutant Proteins)
0 (Proteins)
Entry Date(s):
Date Created: 20201116 Date Completed: 20210126 Latest Revision: 20240330
Update Code:
20250114
PubMed Central ID:
PMC7778892
DOI:
10.1093/nar/gkaa1035
PMID:
33196841
Database:
MEDLINE

Weitere Informationen

ProThermDB is an updated version of the thermodynamic database for proteins and mutants (ProTherm), which has ∼31 500 data on protein stability, an increase of 84% from the previous version. It contains several thermodynamic parameters such as melting temperature, free energy obtained with thermal and denaturant denaturation, enthalpy change and heat capacity change along with experimental methods and conditions, sequence, structure and literature information. Besides, the current version of the database includes about 120 000 thermodynamic data obtained for different organisms and cell lines, which are determined by recent high throughput proteomics techniques using whole-cell approaches. In addition, we provided a graphical interface for visualization of mutations at sequence and structure levels. ProThermDB is cross-linked with other relevant databases, PDB, UniProt, PubMed etc. It is freely available at https://web.iitm.ac.in/bioinfo2/prothermdb/index.html without any login requirements. It is implemented in Python, HTML and JavaScript, and supports the latest versions of major browsers, such as Firefox, Chrome and Safari.
(© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)