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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 contactmaking (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
Bfactor profiles 
Theoretical and experimental Bfactors organized in 5 columns: (i) chain identifier, (ii) residue type, (iii) node index, (iv) GNMbpredicted B factor, and (v) Xray 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 
GNMdefined vibrational entropy (based on Karplus and Kuschik, 1981). 
temp.slowmodes
Slow modes 
23 or more (to represent 40% of the spectrum) columns. The columns 13 list the chain identifier, residue type and node index, respectively; columns 423 (or more) are the corresponding displacements in modes 120 (or more) starting from the slowest (first) mode. 
temp.slow2av
Slow mode average 12 
Cumulative contribution of the slowest two modes to the mobility of residues. The file is organized in 4 columns. The columns 13 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 13 
Same as the above file, except for the last column which describes the cumulative effect of slowest three modes. 
temp.slow10av
Slow mode average 110 
Same as the above file, except for the last column which describes the cumulative effect of slowest ten modes. 
temp.fastmodes
Fast modes 120 
23 columns. The columns 13 list the chain identifiers, residue types and node indices, respectively; columns 423 are the fastest mode shapes starting from the highest mode. Since these modes are highly localized columns 423 have only a few nonzero elements. 
temp.fast10av
Fast mode average 110 
4 columns. The columns 13 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 13 are same as above; columns 423 are the elements of eigenvectors associated with the 20 slowest (lowest frequency) modes, starting from the slowest mode. 
temp.fasteigenvectors
Fast eigenvectors 120 
23 columns. The columns 13 are same as above; columns 423 are the elements of eigenvectors associated with the 20 fastest (highest frequency) modes, starting from the highest mode. 
temp_cc_all.txt
Orientational crosscorrelations 
Orientational crosscorrelations 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.collectivityslow
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 221 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 221 are the corresponding displacements in modes 120 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. 
PRS results files for your structure (in text format)
Filename  Description 
temp_prs_all.txt
PRS matrix 
All elements in the GNMbased 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 13 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 13 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 13 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. 