# FOLD-RATE¶

## Description¶

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

## Instructions¶

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 ssbio.protein.sequence.properties.kinetic_folding_rate.get_foldrate()

## FAQs¶

• 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: http://dx.doi.org/10.1093/nar/gkl043
• 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: http://www.pnas.org/content/114/43/11548.abstract
• 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¶

ssbio.protein.sequence.properties.kinetic_folding_rate.get_foldrate(seq, secstruct)[source]

Submit sequence and structural class to FOLD-RATE calculator (http://www.iitm.ac.in/bioinfo/fold-rate/) to calculate kinetic folding rate.

Parameters: seq (str, Seq, SeqRecord) – Amino acid sequence secstruct (str) – Structural class: all-alpha, all-beta, mixed, or unknown Kinetic folding rate k_f float
ssbio.protein.sequence.properties.kinetic_folding_rate.get_foldrate_at_temp(ref_rate, 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

Parameters: 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 float