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Supplemental Information

Comparison of level-1 conformational clusters obtained in CDR-H3 with North et al., 2011

The cluster medoid/median or representative of the external sets was used for identification of correspondences. Only level-1 clusters with a correspondence are shown here, in order to preserve a readable size for the table (213 total level-1 clusters in CDR-H3). In brackets, next to each correspondence, is the full, level-3, classification in this work of the representative of the external set. The entire correspondence is marked between square brackets and in full-italics because the CDR-H3 definition used in North et al., 2011, was longer by 2 residues (i.e. 93-102).

DOI: 10.7287/peerj.preprints.291v3/supp-1

Rogue CDR sequences

Rogue sequences in every CDR/length, with the respective lists of level-1 cluster-tagged CDRs, in which they are identified.

DOI: 10.7287/peerj.preprints.291v3/supp-2

Minimum sequence distance (mSD) heatmaps

Collection of heatmaps for all CDR/length combinations, showing the minimum number of amino acid differences, position-by-position, between any two sequences of different clusters. allow a quick visual appreciation of the degree of sequence dissimilarity between clusters. mSD heatmaps allow a quick visual appreciation of the degree of sequence dissimilarity between clusters.

DOI: 10.7287/peerj.preprints.291v3/supp-3

Summary for the clustering of CDR-H3

Level-2 clusters are shown exceptionally (marked with an asterisk) when no level-1 cluster is formed (minimum of 2 members required).

DOI: 10.7287/peerj.preprints.291v3/supp-4

Detailed membership assignments (sorted by PDB code)

Csv formatted lists where every CDR is shown in alphabetical PDB order with all available clustering and data-mined information (cis/trans peptides, structure resolution, crystal spacegroup, sequence, Ramachandran logos, cluster core label).

DOI: 10.7287/peerj.preprints.291v3/supp-5

Detailed membership assignments (sorted by cluster)

Csv formatted lists where every CDR is shown in cluster order with all available clustering and data-mined information (cis/trans peptides, structure resolution, crystal spacegroup, sequence, Ramachandran logos, cluster core label).

DOI: 10.7287/peerj.preprints.291v3/supp-6

Additional Information

Competing Interests

The authors report no competing interests.

Author Contributions

Dimitris Nikoloudis conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Jim E. Pitts contributed reagents/materials/analysis tools, reviewed drafts of the paper, expert advice, general project supervision.

José W. Saldanha conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper, expert advice, general project supervision.

Funding

The authors declare no external funding sources.


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