dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions
Abstract
Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acid complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.
- Authors:
-
- Anhui Univ., Hefei, Anhui (China). School of Life Sciences
- Shanghai Jiao Tong Univ. (China). State Key Lab. of Microbial Metabolism and School of Life Sciences and Biotechnology
- Dalian Univ., Dalian, Liaoning (China). Information and Engineering College
- Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry; Univ. of Wisconsin, Madison, WI (United States). Dept. of Mathematics; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE; National Natural Science Foundation of China (NSFC)
- OSTI Identifier:
- 1435258
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Database
- Additional Journal Information:
- Journal Volume: 2018; Journal Issue: 1; Related Information: See also https://academic.oup.com/database/article/doi/10.1093/database/bay034/4959188; Journal ID: ISSN 1758-0463
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Liu, Ling, Xiong, Yi, Gao, Hongyun, Wei, Dong-Qing, Mitchell, Julie C., and Zhu, Xiaolei. dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions. United States: N. p., 2018.
Web. doi:10.1093/database/bay034.
Liu, Ling, Xiong, Yi, Gao, Hongyun, Wei, Dong-Qing, Mitchell, Julie C., & Zhu, Xiaolei. dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions. United States. https://doi.org/10.1093/database/bay034
Liu, Ling, Xiong, Yi, Gao, Hongyun, Wei, Dong-Qing, Mitchell, Julie C., and Zhu, Xiaolei. Mon .
"dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions". United States. https://doi.org/10.1093/database/bay034. https://www.osti.gov/servlets/purl/1435258.
@article{osti_1435258,
title = {dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions},
author = {Liu, Ling and Xiong, Yi and Gao, Hongyun and Wei, Dong-Qing and Mitchell, Julie C. and Zhu, Xiaolei},
abstractNote = {Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acid complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.},
doi = {10.1093/database/bay034},
journal = {Database},
number = 1,
volume = 2018,
place = {United States},
year = {Mon Apr 02 00:00:00 EDT 2018},
month = {Mon Apr 02 00:00:00 EDT 2018}
}
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Anatomy of hot spots in protein interfaces
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Hot spots in protein–protein interfaces: Towards drug discovery
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Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein–Protein and Protein–Nucleic Acid Interfaces
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Computational Alanine Scanning Mutagenesis—An Improved Methodological Approach for Protein–DNA Complexes
journal, August 2013
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Thermodynamic database for protein-nucleic acid interactions (ProNIT)
journal, November 2001
- Prabakaran, P.; An, J.; Gromiha, M. M.
- Bioinformatics, Vol. 17, Issue 11
BIPA: a database for protein–nucleic acid interaction in 3D structures
journal, April 2009
- Lee, Semin; Blundell, Tom L.
- Bioinformatics, Vol. 25, Issue 12
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions
journal, January 2006
- Kumar, M. D. S.
- Nucleic Acids Research, Vol. 34, Issue 90001
A series of PDB-related databanks for everyday needs
journal, October 2014
- Touw, Wouter G.; Baakman, Coos; Black, Jon
- Nucleic Acids Research, Vol. 43, Issue D1
An updated version of NPIDB includes new classifications of DNA–protein complexes and their families
journal, December 2015
- Zanegina, Olga; Kirsanov, Dmitriy; Baulin, Eugene
- Nucleic Acids Research, Vol. 44, Issue D1
Probing binding hot spots at protein–RNA recognition sites
journal, September 2015
- Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao
- Nucleic Acids Research, Vol. 44, Issue 2
A hot spot of binding energy in a hormone-receptor interface
journal, January 1995
- Clackson, T.; Wells, J.
- Science, Vol. 267, Issue 5196
Works referencing / citing this record:
A structure-based model for the prediction of protein–RNA binding affinity
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