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¶
- Obtain your protein’s sequence
- Determine the main secondary structure composition of the protein (
all-alpha
,all-beta
,mixed
, orunknown
) - 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
, orunknown
Returns: Kinetic folding rate k_f
Return type: 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
Returns: Kinetic folding rate k_f at temperature T
Return type: float
- ref_rate (float) – Kinetic folding rate calculated from the function