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. 2023 May 4;39(5):btad260.
doi: 10.1093/bioinformatics/btad260.

RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics

Alessio Del Conte  1 , Alexander Miguel Monzon  2 , Damiano Clementel  1 , Giorgia F Camagni  1 , Giovanni Minervini  1 , Silvio C E Tosatto  1 , Damiano Piovesan  1
Affiliations

RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics

Alessio Del Conte et al. Bioinformatics. .

Abstract

RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software, with structural clustering to enhance the analysis and visualization of the conformational complexity. It combines precise calculation of non-covalent interactions with the power of PyMOL to manipulate and visualize protein structures. The plugin identifies and highlights correlating contacts and interaction patterns that can explain structural allostery, active sites, and structural heterogeneity connected with molecular function. It is easy to use and extremely fast, processing and rendering hundreds of models and long trajectories in seconds. RING-PyMOL generates a number of interactive plots and output files for use with external tools. The underlying RING software has been improved extensively. It is 10 times faster, can process mmCIF files and it identifies typed interactions also for nucleic acids.

Availability and implementation: https://github.com/BioComputingUP/ring-pymol.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
RING-PyMOL analysis of a MD simulation. Snapshots have been derived from a simulation of the STIM1 protein (PDB 2K60) run for 100 ns and sampled every 0.8 ns generating 125 states. (A) Cluster assignments for all states. Different colors represent different clusters. The yellow layout indicates those states shown in (B). The legend indicates the states selected as clusters representatives. (B) RMSD-based structural hierarchy visualized as a dendrogram. The clustering, using default parameters and 2.5 Å cutoff, generated 16 different clusters. The dashed line indicates the cutoff (5.5 Å) used to select the representative conformations shown in (C). (C) Patterns of π–π and π–cation interactions in the selected conformations. Interacting residues are displayed as sticks and colored by element, different states show different contact patterns.
See this image and copyright information in PMC

References

    1. Clementel D, Del Conte A, Monzon AM et al RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles. Nucleic Acids Res 2022;50:W651–6. - PMC - PubMed
    1. Liang Z, Verkhivker GM, Hu G et al Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications. Brief Bioinform 2020:21:815–35. - PubMed
    1. Martin AJM, Vidotto M, Boscariol F et al RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics 2011;27:2003–5. - PubMed
    1. Piovesan D, Minervini G, Tosatto SCE et al The RING 2.0 web server for high quality residue interaction networks. Nucleic Acids Res 2016;44:W367–74. - PMC - PubMed
    1. Schrödinger LLC. (2015) The PyMOL molecular graphics system, version 2.5.

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