ProNAB

Database for binding affinities of protein-nucleic acid complexes and their mutants

ProNAB

ProNAB, a database on binding affinity of protein-nucleic acid complexes. ProNAB, which contains 20 219 entries on dissociation constant (Kd), binding free energy change (ΔG), experimental conditions, sequence, structure and literature information. Additional features include the options to search, display, visualization, download and upload the data.

Users can search for a specific protein, Nucleic acid, affinity values (Kd), a range of ΔG values, ΔΔG values for a specific mutation, secondary structure and accessible surface area (ASA). Please check our tutorial for help on searching the database. Have questions? Please see our FAQs page. If you would like to access the entire dataset, please contact us. Thank you for visiting ProNAB.

What's New

  •  Feb 2023: Updated the database with 129 binding affinity data from recent literature. 
  •  Jan 2023: Updated the Download page. 
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    TUTORIAL




    • ★Tutorial 1: Identify amino acid single mutations, which increase the binding affinity (ΔΔG < 0 kcal/mol).

    ★Tutorial 2: Retrieve ΔG of protein-DNA complexes obtained at pH 7 and temperature at 298 K.


    ★Tutorial 3: Obtain ΔΔG of Alanine mutations (To Ala) and display the results in descending order.

    ★Tutorial 4: ​​Get ΔΔG of nucleotide double mutations in protein-RNA complexes and display the results in ascending order.

    ★Tutorial 5: ​Retrieve ΔΔG value of amino acid single mutations located in alpha helical regions.

    FREQUENTLY ASKED QUESTIONS




    What is ProNAB?

    ProNAB is a searchable database of thermodynamic data (including dissociation rate, binding free energy change) for mutant and wild-type in protein-Nucleic acid complexes. It contains more than 20 000 experimental data from published literature. The current version contains entries with 802 protein-DNA and 340 protein-RNA complexes with strucutal information. ProNAB links structural and sequence data to PDB and UniProt respectively.

    How are mutations denoted in each entry?

    The mutations are specified using the format "wild-type residue - position - mutated residue". For example, a mutation on the 2nd position would be represented as "C2S", where Cys (C) is the wild-type residue in the 2nd position, mutated to Ser (S). Double and triple mutants are denoted in the same with the separator in between (E.g. M321A ; Q325A). Deleted regions are mentioned by the region name or residues mentioned with position number (E.g. Del G172).

    How to download the data?

    THe database provides option to download the search results. Users can click the "Download Now" below the search result to dowload the results. If you are in need of entire dataset, Kindly fill your details in the download page.

    What are the different types of mutations available in ProNAB?

    We have included single, double, multiple mutations along with deletions and insertions in both proteins and nucleic acids

    Glossary of terms

    Terms Explanation
    Entry ID Each entry of the ProNAB database is provided with a unique ID.The results are obtained on giving the specific ID
    Keyword Any Keyword like protein name (cro) / nucleic acid name (OR1 operator), etc can be given.
    ASA Accessible Surface Area of free protein and protein-nucleic acid complex is provided
    RSA Relative Surface Accessibility of free protein and protein-nucleic acid complex is provided. We classifed the residues with less than 20% accessibility as buried, between 20% and 50% as partially buried and more than 50% as exposed.
    Sec str Secondary Structural Information for the mutation site (Helix, Strand, Coil and Turn)
    PDB free PDB (Protein Data Bank) ID of the free protein (apo form of protien without nucleic acid)
    PROSITE ID PROSITE ID of the motif present in the protein is given
    DisProt ID DisProt ID of the protein is given
    GenBank ID GenBank ID corresponding to the nucleic acid is provided
    NDB ID NDB ID of the protein-nucleic acid complex is given
    PDB complex PDB (Protein Data Bank) ID of the protein-nucleic acid complex
    Kd Dissociation rate constant
    Ka Association rate constant ; Inverse of Dissociation constant
    ΔG Change in binding free energy; Calculated using the formula -RTln(Kd)
    ΔΔG Difference in binding free energy change between mutant and wild-type complex
    T Temperature used in the measurement of thermodynamic values
    pH pH used in the measurement of thermodynamic values
    Method Experimental method used for the measurement of thermodynamic values
    Stoichiometry Stoichiometry of binding of protein-nucleic acid complex
    PubMed ID Each entry in linked to a PubMed ID of the article which the reports the specific data

    Contact Us

    ★ This database is under constant development. We always welcome contributions of published, relevant data from authors. If data is missing or incorrect, please contact us. We appreciate your feedback and suggestions for improvement.
    Prof. M. Michael Gromiha
    Protein Bioinformatics Lab
    Department of Biotechnology
    Indian Institute of Technology, Madras
    Email : gromiha@iitm.ac.in
    Website: Protein Bioinformatics Lab
    K. Harini
    Ph.D. Scholar
    Protein Bioinformatics Lab
    Department of Biotechnology
    Indian Institute of Technology, Madras
    Email : ulianukannan@gmail.com




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    Usage Notice

    The use of this database implies you are aware of and in agreement with the disclaimer provided below:

    ★ This database is meant for educational and research purposes only. It is a non-profit service to the scientific community. In case of use by industries, kindly contact principle investigator Prof.M. Michael Gromiha (gromiha@iitm.ac.in). We make no warranties regarding the correctness of the data, and disclaim liability for damages resulting from its use.Further, the developers and authors are not liable for the accuracy or completeness of any information and data residing in the external links. Please read the disclaimers and usage notices of the respective linked websites and databases carefully.

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