Published June 23, 2021 | Version v1
Dataset Open

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"

  • 1. University of Trento


June 23, 2021

Thomas Tarenzi, Marta Rigoli and Raffaello Potestio


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).


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Additional details


VARIAMOLS – VAriable ResolutIon Algorithms for macroMOLecular Simulation 758588
European Commission