Dataset Open Access

Project files provided as supporting information to the manuscript "How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study"

Thomas Tarenzi; Marta Rigoli; Raffaello Potestio

June 23, 2021

Thomas Tarenzi, Marta Rigoli and Raffaello Potestio

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The dataset contains the following folders:

- contact_area_binding_site: files with the computed surface area, used for the calculation of the contact area between PD-1 and the antibody Fab (Fig. S41).

- hbonds_ab-pd1: number of hydrogen bonds between the antigen and the antibody, for each holo cluster (Fig. S41).

- mutual_information: matrices with the computed mutual information, for each pair of residues (Fig. S34, S35, S46). The folder contains also the generalized correlation coefficients (Fig. S43) and the correlation scores (Fig. 4, S44, S45), computed from the mutual informations.

- networks: communities - for each cluster, each residue is assigned to a community within the interaction network (Fig. S32, S33). betweenness - the values of edge betweenness for each cluster (S30, S31).

- output_clustering: each frame of the apo and holo simulations is assigned a cluster index, on the basis of the structural similarity (Fig. S4).

- PAD: per-residue values of PAD parameter, for apo and holo systems (Fig. 3, S39).

- PCA: principal component analysis for each conformational cluster (Section S2.1).

- representative_structures: representative structures for each conformational cluster (Fig. 2).

- r_gyr_antibody: radii of gyration of the antibody, for each cluster (Fig. 2).

- r_gyr_hinge: radii of gyration of the sole hinge segment, for each cluster (Fig. S36).

- RMSD_antibody: distributions of the root-mean-square deviation of the antibody, for each cluster (Fig. S5). 

- RMSD_antigen: root-mean-square deviation of the antigen PD-1, for each cluster (Fig. S42).

- RMSD_binding_site: distributions of the root-mean-square deviation of the residues belonging to the paratope, for each cluster (Fig. S40, S47).

- RMSD_matrix: root-mean-square deviation between structures belonging to different pairs of clusters (Fig. S9).

- rmsf_antigen: root-mean-square fluctuation of the antigen PD-1, for each cluster (Fig. S42).

- rmsf_hinge: difference between the total root-mean-square fluctuations of the two hinge segments, for each cluster (Fig. S38).

- salt_bridge: distribution of distances between residues R979 and D1377 (Fig. 4).

- sasa_domains: contact area between Fab and Fc antibody domains, for each cluster (Fig. S8).

- sasa_hinge: solvent accessible surface area of each hinge segment, for each cluster (Fig. S37).

Files (1.4 GB)
Name Size
contact_area_binding_site.zip
md5:a5fd42a651e17279abbd7167471be846
319.5 kB Download
hbonds_ab-pd1.zip
md5:a2420e0e5d91d341c5579d69aa389603
334.4 kB Download
mutual_information.zip
md5:93e4be37a6ee16f752e2850b52ab7990
135.6 MB Download
networks.zip
md5:5c91acbc0da931628ee6471b5aecb71d
1.0 MB Download
output_clustering.zip
md5:ac3ed2c1f4bab23b745864255fce5836
425.5 kB Download
PAD.zip
md5:ef6356968c4475a1352a4055818f23af
46.2 kB Download
PCA.zip
md5:145639c406afb70cb58d6e7a6b65f54a
1.3 GB Download
r_gyr_antibody.zip
md5:f4db64de769e93fc1349dfb18d733353
3.1 MB Download
r_gyr_hinge.zip
md5:dc9a565169f1f8b0ea27e4a991823ef8
3.3 MB Download
README
md5:2ca9a05eeb3821581215d2e41afa6463
2.4 kB Download
representative_structures.zip
md5:4eeb11e3b2236f31b628abfd07a086cf
3.1 MB Download
RMSD_antibody.zip
md5:23e877d3453a3b631d287ed81d81295a
1.4 MB Download
RMSD_antigen.zip
md5:714261fb61f219acab5dbcb86596f664
643.6 kB Download
RMSD_binding_site.zip
md5:00c2bfa59e7b8c0b8b5154e0eb7b2a69
1.6 MB Download
RMSD_matrix.zip
md5:5a28fcc2c729008bafc7164430993c25
14.4 MB Download
rmsf_antigen.zip
md5:509cd7169397ed8f70aab88ebd0e3213
7.8 kB Download
rmsf_hinge.zip
md5:f0413a78efde674b4359a79f406413a6
15.9 kB Download
salt_bridge.zip
md5:fdf04082da496e8ab5b044595f381b1c
1.1 MB Download
sasa_domains.zip
md5:1f9c5ffbada77b101b66bd029dda43cd
844.6 kB Download
sasa_hinge.zip
md5:12c67aa274069ab1120c266735a6daf4
1.9 MB Download
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