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. |