This module provides a function to predict the kinetic folding rate (kf) given an amino acid sequence and its structural classficiation (alpha/beta/mixed).


  1. Obtain your protein’s sequence
  2. Determine the main secondary structure composition of the protein (all-alpha, all-beta, mixed, or unknown)
  3. Input the sequence and secondary structure composition into the function


  • What is the main secondary structure composition of my protein?

    • all-alpha = dominated by α-helices; α > 40% and β < 5%
    • all-beta = dominated by β-strands; β > 40% and α < 5%
    • mixed = contain both α-helices and β-strands; α > 15% and β > 10%
  • What is the kinetic folding rate?

    • Protein folding rate is a measure of slow/fast folding of proteins from the unfolded state to native three-dimensional structure.
  • What units is it in?

    • Number of proteins folded per second
  • How can I install FOLD-RATE?

    • FOLD-RATE is only available as a web server. ssbio provides a wrapper for the web server and allows you to submit protein sequences to it along with caching the output files.
  • How do I cite FOLD-RATE?

    • Gromiha MM, Thangakani AM & Selvaraj S (2006) FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucleic Acids Res. 34: W70–4 Available at:
  • How can this parameter be used on a genome-scale?

    • See: Chen K, Gao Y, Mih N, O’Brien EJ, Yang L & Palsson BO (2017) Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proceedings of the National Academy of Sciences 114: 11548–11553 Available at:
  • I’m having issues running FOLD-RATE…

    • See the ssbio wiki for (hopefully) some solutions - or add yours in when you find the answer!

API, secstruct)[source]

Submit sequence and structural class to FOLD-RATE calculator ( to calculate kinetic folding rate.

  • seq (str, Seq, SeqRecord) – Amino acid sequence
  • secstruct (str) – Structural class: all-alpha`, all-beta, mixed, or unknown

Kinetic folding rate k_f

Return type:

float, new_temp, ref_temp=37.0)[source]

Scale the predicted kinetic folding rate of a protein to temperature T, based on the relationship ln(k_f)∝1/T

  • ref_rate (float) – Kinetic folding rate calculated from the function get_foldrate()
  • new_temp (float) – Temperature in degrees C
  • ref_temp (float) – Reference temperature, default to 37 C

Kinetic folding rate k_f at temperature T

Return type: