Table 2.

Features of MDM-TASK-web and other servers used to analyse static and dynamic protein structures.

Functionality	MDM-TASK-web	NAPS	ANCA	RIP-MD	MDN
Input file formats	Tools processing trajectories require a topology and a trajectory, both in multiple formats. PRS uses PDB files as conformations.	PDB topology and DCD trajectory file.	Single PDB files.	PDB or PSF formats. Trajectories are loaded as a multi-PDB file.	All files used by GROMACS to analyse a trajectory are needed for analyses.
Residue interaction network (RIN) from MD	Dynamic residue networks analysis via averaged network centralities from RINs.	Networks are aggregated to one from an MD simulation.	–	RIN for each frame	Network coupling, betweenness
Residue interaction network from a single structure	RIN is calculated for a single protein structure.	RIN is calculated for single protein structure.	Amino acid network (AAN) for single structure.	RIN is calculated for single protein structure.	Single network is calculated from interaction energies from MD.
Network metrics	Averaged network centrality metrics for betweenness, degree, eccentricity, averaged shortest paths, closeness, Katz, PageRank and eigencentrality. Same metrics are available for single conformations.	Degree, closeness, betweenness, clustering coefficient, eccentricity, shortest paths, k-cliques, eigenspectra.	Degree, closeness, betweenness, clustering coefficient, average shortest path, edge betweenness.	–	Non-normalized and normalised node betweenness.
Network node types	Cβ and glycine Cα atoms.	Cβ and glycine Cα atoms, amino acids.	Cα atoms.	Cα atoms, residues.	Amino acids.
Network edge types	Any node < 6.7Ang to any other node.	DCC, energy, inverse distance.	Contact energy, Cα cut-off distance.	Cα contacts, H-bonds, salt-bridges, disulfide bonds, cation-π, π–π, Arg–Arg distance, Coulombic, and Lennard Jones.	Averaged inter-residue interaction energy.
Weighted residue contact network and heat map	Weighted contacts at a single locus. Contact heat map also aggregates residue contacts from multiple simulations for large-scale comparisons of single loci.	2D dot matrix.	Implements a node-weighted amino acid contact energy network, and an edge-weighted amino acid contact energy network.	–	The edge weights for the network are derived from the energy involved in residue interactions.
Dynamic Cross Correlation	Normalised residue covariance matrix. Supports nucleic acids.	Normalised residue covariance matrix.	–	Pearson correlations of interactions	–
Perturbation Response Scanning	Scanning of hotspot residues leading to a target conformational change.	–	–	–	–
Essential dynamics (ED)	Several algorithms for visually assessing conformational distributions from MD simulations: t-SNE, internal PCA, comparative ED, multidimensional scaling.	–	–	–	–
Normal Mode Analysis (NMA)	Elastic network model to extract global motions and compute MSF from a single PDB-formatted file. NMA is also computed from MD trajectories.	–	–	–	–
Coordination propensity	Identifies residue pairs whose distance vary the most.	–	–	–	–