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GNM results files for your structure (in text format) Help

Filename	Description
temp_nodes.pdb GNM nodes	Structural data on GNM nodes, in PDB format.
temp_connectivity.txt Network topology	The type of connectivity (topology) in the examined structure. The file is organized in three columns: the first two are the indices of the connected nodes, and the third designates the type of connection. Designations 1, 2 and 3 refer to amino acid pairs, nucleotides pairs and amino acid – nucleotide pairs, respectively. If the file contains multiple chains, nodes indices are assigned starting from 1 for chain A, and continuing sequentially with chains B, C, etc as listed in the PDB file.
temp.kdat GNM Kirchhoff matrix	The GNM Kirchhoff matrix Γ written in three columns. The first two are the indices i and j of contact-making (or connected) nodes, and the third is the corresponding element Γ_ij of Γ (i.e. -1 if i ≠ j, and coordination number or node degree if i = j).
temp.cont Coordination number of nodes	The file consists of four columns: (i) residue type, (ii) chain identifier, (iii) node index, and (iv) coordination number of the corresponding node.
temp.bfactor B-factor profiles	Theoretical and experimental B-factors organized in 5 columns: (i) chain identifier, (ii) residue type, (iii) node index, (iv) GNMbpredicted B- factor, and (v) X-ray crystallographic B factor.
temp.eigen Eigenvalues	The eigenvalues corresponding to the examined structure, organized in ascending order. The 1^st is the zero eigenvalue.
temp_entropy.txt Vibrational entropy	GNM-defined vibrational entropy (based on Karplus and Kuschik, 1981).
temp.slowmodes Slow modes	23 or more (to represent 40% of the spectrum) columns. The columns 1-3 list the chain identifier, residue type and node index, respectively; columns 4-23 (or more) are the corresponding displacements in modes 1-20 (or more) starting from the slowest (first) mode.
temp.slow2av Slow mode average 1-2	Cumulative contribution of the slowest two modes to the mobility of residues. The file is organized in 4 columns. The columns 1-3 columns list the chain identifier, residue type and corresponding node index; and column 4 is the square displacement driven by the these slowest two modes.
temp.slow3av Slow mode average 1-3	Same as the above file, except for the last column which describes the cumulative effect of slowest three modes.
temp.slow10av Slow mode average 1-10	Same as the above file, except for the last column which describes the cumulative effect of slowest ten modes.
temp.fastmodes Fast modes 1-20	23 columns. The columns 1-3 list the chain identifiers, residue types and node indices, respectively; columns 4-23 are the fastest mode shapes starting from the highest mode. Since these modes are highly localized columns 4-23 have only a few non-zero elements.
temp.fast10av Fast mode average 1-10	4 columns. The columns 1-3 are same as above; column 4 lists the residue square fluctuations driven by 10 highest frequency modes.
temp.sloweigenvectors Slow eigenvectors	23 columns. The columns 1-3 are same as above; columns 4-23 are the elements of eigenvectors associated with the 20 slowest (lowest frequency) modes, starting from the slowest mode.
temp.fasteigenvectors Fast eigenvectors 1-20	23 columns. The columns 1-3 are same as above; columns 4-23 are the elements of eigenvectors associated with the 20 fastest (highest frequency) modes, starting from the highest mode.
temp_cc_all.txt Orientational cross-correlations	Orientational cross-correlations between residue fluctuations. The values vary from -1 (fully anticorrelated motions) to +1 (fully correlated). The file is provided for structures having no more than 1,000 nodes.
temp.collectivity-slow Degree of collectivity	The degree of collectivity is listed for N/10 (N is the total number of nodes) or at least 20 slowest modes.

ANM results files for your structure (in text format)

Filename	Description
temp_ANM.slowevs Slow eigenvectors	21 columns. The 1st column list the node index; columns 2-21 are the elements of eigenvectors associated with the 20 slowest (lowest frequency) modes, starting from the slowest (first) mode. Each node has three rows for x, y and z dimensions.
temp_ANM.slwmodes Slow modes	21 columns. The 1st column list the node index; columns 2-21 are the corresponding displacements in modes 1-20 starting from the slowest (first) mode.
temp_ANM.xyz ANM motions	The ANM motion of the 20 slowest modes in xyz format, starting from the slowest mode.
temp_ANM.eigenval_all Eigenvalues	The eigenvalues corresponding to the examined structure, organized in ascending order. The first six values are the zero eigenvalue.
temp.time ANM_Time	Estimated timescale of ANM modes using the general power law: $56.0741\times\lambda_{i}^{-1.6015}$ [Chan et al. 2019] where $\lambda_{i}$ is the ANM's i-th eigenvalue.

PRS results files for your structure (in text format)

Filename	Description
temp_prs_all.txt PRS matrix	All elements in the GNM-based PRS matrix; the index of rows and columns are indices for those nodes triggered by others and nodes trigger the responses (accept perturbation), respectively.
temp_mean_prs_all.txt Mean profiles	5 columns. The columns 1-3 list the chain identifiers, residue types and node indices, respectively; columns 4 and 5 are the elements of average response of effectors (triggered by others) and sensors (triggered by themselves), respectively.

Hitting time results files for your structure (in text format)

Filename	Description
temp_hit_hitting.txt Hitting time matrix	All elements in the hitting time matrix; the index of rows and columns are indices for those residues receiving signals and residues broadcasting signals, respectively.
temp_hit_hitting_all.txt Mean hitting times	7 columns. The columns 1-3 list the chain identifiers, residue types and node indices, respectively; columns 4 and 5 are the elements of average hitting time of receivers (receiving signals efficiently, perturbation sites) and broadcasters (sending signals efficiently, response sites), respectively; columns 6 and 7 are the elements of the standard deviation of average hitting time of receivers and broadcasters, respectively.
temp_hit_hitting_norm.txt Hitting rate matrix	All elements in the hitting rate matrix; the index of rows and columns are indices for those residues receiving signals and residues broadcasting signals, respectively.
temp_hit_hitting_all_norm.txt Mean hitting rates	7 columns. The columns 1-3 list the chain identifiers, residue types and node indices, respectively; columns 4 and 5 are the elements of average hitting rate of receivers (receiving signals efficiently, perturbation sites) and broadcasters (sending signals efficiently, response sites), respectively; columns 6 and 7 are the elements of the standard deviation of average hitting rate of receivers and broadcasters, respectively.