Journal
NUCLEIC ACIDS RESEARCH
Volume 50, Issue D1, Pages D1528-D1534Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkab848
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Funding
- Indian Institute of Technology, Madras
- Science and Engineering Research Board (SERB), Ministry of Science and Technology, Government of India [CRG/2020/000314]
- IIT Madras and Department of Science and Technology, Government of India
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ProNAB is a database containing over 20,000 experimental data for the binding affinities of protein-DNA and protein-RNA complexes, with detailed information and a user-friendly interface. The database facilitates the study of protein-nucleic acid interactions, development of prediction tools, and design of complexes with specific affinities.
Protein-nucleic acid interactions are involved in various biological processes such as gene expression, replication, transcription, translation and packaging. The binding affinities of protein-DNA and protein-RNA complexes are important for elucidating the mechanism of protein-nucleic acid recognition. Although experimental data on binding affinity are reported abundantly in the literature, no well-curated database is currently available for protein-nucleic acid binding affinity. We have developed a database, ProNAB, which contains more than 20 000 experimental data for the binding affinities of protein-DNA and protein-RNA complexes. Each entry provides comprehensive information on sequence and structural features of a protein, nucleic acid and its complex, experimental conditions, thermodynamic parameters such as dissociation constant (K-d), binding free energy (Delta G) and change in binding free energy upon mutation (Delta Delta G), and literature information. ProNAB is cross-linked with GenBank, UniProt, PDB, ProThermDB, PROSITE, DisProt and Pubmed. It provides a user-friendly web interface with options for search, display, sorting, visualization, download and upload the data. ProNAB is freely available at https://web.iitm.ac.in/bioinfo2/pronab/ and it has potential applications such as understanding the factors influencing the affinity, development of prediction tools, binding affinity change upon mutation and design complexes with the desired affinity.
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