What is tFolder? tFolder is a software for predicting the coarse grained folding pathways of β-sheet proteins. It will help you to identify β-sheet folding intermediates.
What tFolder is not? tFolder is not a substitute for molecular dynamics tools. tFolder predicts residue contacts but do not provide atomistic details neither velocity information. tFolder does not predict α-helices.
When should I use tFolder? tFolder is fast. You can use it if you just need to predict critical steps of the folding pathways. It also enables you to study (at a coarse grained level) the folding dynamics of large protein sequences.
How accurate is the tFolder? In order to improve the time complexity, we use a residue level representation of the protein structure that may ignore few energetic barriers between folding intermediates.
What is the maximal input size? Currently, we reccomend to use tFolder on protein with at most 100 residues and with a β-sheet that does not contain more than 6 β-strands.
What are the input parameters? Beside the protein sequence, you can also specify the minimal and maximal length of the β-strands, the minimal number of residue between two consecutive β-strand, and the maximal number of β-strands in the β-sheet.
What is the output? tFolder predictions include a dynamic of the various folding intermediates (i.e. density of state over time) and a approximate energy folding landcsape.