The files used in different analysis reported in the manuscript titled - 'A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains' are shared at two locations. Following is a brief description of these files.

Location - https://github.com/DunbrackLab/Kinases

1. HMM profile files - HMM files for each of the nine groups computed separately labeled as Groupname.hmm, like AGC.hmm
2. HMM profile file - HMM file computed from the full alignment including all the sequences - Human-PK.hmm
3. Score files - HMM scores of each kinase sequence against all the groupwise HMMs both for iteration1 (HMM-iter1-scores-tables.txt) and iteration2 (HMM-iter1-scores-tables.txt)
4. Jalview session file - Kinase alignment with sequences colored by secondary structure information from PDB file if the structure is known; or predicted secondary structure if the experimental structure is not known. The file could be opened in Jalview - kinases-PDB-SSPred.jvp

Location - https://zenodo.org/record/3445533

1. The file contains list of residue pairs aligned in pairwise structural alignments of 272 human protein kinases which were used as a benchmark in the study. The alignments were created by FATCAT and optimized by SE program.