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dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

Journal Article · · Database
 [1];  [2];  [3];  [2];  [4];  [1]
  1. Anhui Univ., Hefei, Anhui (China). School of Life Sciences
  2. Shanghai Jiao Tong Univ. (China). State Key Lab. of Microbial Metabolism and School of Life Sciences and Biotechnology
  3. Dalian Univ., Dalian, Liaoning (China). Information and Engineering College
  4. 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
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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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE; National Natural Science Foundation of China (NNSFC)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1435258
Journal Information:
Database, Journal Name: Database Journal Issue: 1 Vol. 2018; ISSN 1758-0463
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (3)

Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification journal February 2020
A structure-based model for the prediction of protein–RNA binding affinity journal August 2019
Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes journal August 2018

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59 BASIC BIOLOGICAL SCIENCES