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. Author manuscript; available in PMC: 2023 Jul 13.
Published in final edited form as: Methods Mol Biol. 2023;2627:41–59. doi: 10.1007/978-1-0716-2974-1_3

Table 1.

Selected publicly accessible threading methods that implicitly or explicitly use contact information

Name (reference) Method Availability
PROSPECT (Xu and coworkers [46]) Divide-and-conquer algorithm http://compbio.ornl.gov/structure/prospect/
PROSPECTOR (Skolnick and coworkers [75, 76]) Hierarchical approach http://bioinformatics.danforthceneter.org/services/threading.html
RAPTOR (Xu and coworkers [14]) Linear programming http://www.cs.uwaterloo.ca/~j3xu/RAPTOR_form.htm
EigenTHREADER (Jones and coworkers [20]) Dynamic programming and eigendecomposition http://bioinfadmin.cs.ucl.ac.uk/downloads/eigenTHREADER/
map_align (Baker and coworkers [62]) Iterative double dynamic programming https://github.com/sokrypton/map_align
CEthreader (Zhang and coworkers [63]) Dynamic programming and eigendecomposition https://zhanglab.ccmb.med.umich.edu/CEthreader/
CATHER (Yang and coworkers [64]) Iterative double dynamic programming https://yanglab.nankai.edu.cn/CATHER/
ThreaderAI (Shen and coworkers [65]) Deep residual neural network and dynamic programming https://github.com/ShenLab/ThreaderAI