Pathfinder

Pathfinder performs large-scale sampling of the conformational space and clusters the decoys obtained in the sampling. The heterogeneous conformations obtained by clustering are named seed states. Then, a resampling algorithm that is not constrained by the local energy basin is designed to obtain the transition probabilities of seed states. Finally, protein folding pathways are predicted based on seed state transition probabilities. The results reveal some protein folding mechanism, which is show in Example.

Pathfinder Sever ( It is recommended that you use the PAthreader server. )

Input the sequence(mandatory):

Please copy and paste your sequence file here in FASTA format . Load example

Or upload the sequence file:

Input the fragment library(mandatory):

Pathfinder needs to get fragment library files from Robetta server

Please copy and paste your 3 fragment library here. Load example

Or upload the seqence file:

Please copy and paste your 9 fragment library here. Load example

Or upload the seqence file:

Input the native structure(optional):

Please copy and paste your native file here in PDB format , load example

Or upload the seqence file:

User information

Email: (mandatory, where results will be sent to)

Job name: (optional, your given name to this job)

References

Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao and Guijun Zhang. Pathfinder: protein folding pathway prediction based on conformational sampling. PLOS Computational Biology, 19(9): e1011438, 2023.

guijunzhanglab@163.com