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| Mutagenesis |
| Coloring by b-factor values × | ||||||
| Coloring by secondary structure × | ||
Helix |
Sheet |
Loop |
| Coloring by centrality values × | ||||||
| Coloring by conservation score × | ||||||||||
N/A |
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Some features are disabled!
The network has more than one component. Global parameters and centrality analysis are not supported for such networks.
Try changing the threshold to construct one connected component.
Some features are disabled!
This function is only available for the custom PDB file.
Some features are disabled!
This function is not available for the selected edge weight type.
This function is only available when Normal Mode Analysis cross correlations are used as edge weight.
Some features are disabled!
Conservation scores are not available for the selected structure.
Some features are disabled!
This function is not available for atom-pair or interaction strength network type.
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| Source | Target | Custom Energy |
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| Centrality values normalized with respect to maximum × | |||||||||
≤ 0.1 | ≤ 0.2 |
≤ 0.3 | ≤ 0.4 | ≤ 0.5 |
≤ 0.6 | ≤ 0.7 | ≤ 0.8 |
≤ 0.9 | ≤ 1.0 |
Download: xlsx
| Residue | Clustering coefficient |
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Download: xlsx
| Node | Eccentricity |
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Download: xlsx
| Node | Degree |
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Topological Parameters
| Help mode | Distance calculation | ||
| Display residue mode | Neighboring residues | ||
| Uniprot annotations | |||
| Show secondary structure | Show 3D network |
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| 3D Structure Coloring |
Edge Coloring |
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| Alternative paths× |
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Edge Weight
Display Map
Residue Metrics
| Square Fluctuations | |||
| Sequence Conservation Scores | |||
| B-factors |
| Centrality | Normalize | Sort by | |
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k-clique Analysis
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Threshold
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Cutoff
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How to cite:
Rasim Murat Aydınkal, Onur Serçinoğlu, Pemra Ozbek, ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism, Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019, Pages W471–W476, doi: 10.1093/nar/gkz390.
| OS | Version | Chrome | Firefox | Microsoft Edge | Safari |
| MacOS | Mojave | 72.0.3626.109 | 65.0.1 | N/A | 12.0.2 |
| Windows | 7 | 72.0 | 64.0 | not tested | N/A |
| Linux | 4.15.0-45 | not tested | 65.0 | N/A | N/A |
System Requirements
There are no system requirements. There is no installation or login requirement.
Q1. Page goes unresponsive after a while. It doesn’t work.
A1. Click wait, it is probably due to the limitations of your own computer.
Q2. the tool does not let me choose the conservation score option for coloring.
A2. The conservation data is missing in the CONSURF-DB. The user can upload their own data.
Q3. B-factor coloring option is disabled, why?
A3. Check your PDB. B-factor values are either missing or the values are all equal to each other.
Q4. I am trying to do PDBj analysis for my network, but the server does not let me do this and give me a warning as: ‘disabled for this pdb’. What is the reason?
A4. this might be caused due to one of the following reasons:
- The values might be missing in the databank.
- PDBj does not support homodimers.
- PDBj option can not be chosen for custom PDBs.
We have developed a web-based application called ProSNex (Protein Structure Network Explorer) which provides a novel and enhanced analysis of protein structures using network formalism. It provides a wide range of data and visualization options.
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Rasim Murat Aydinkal a.rasimmurat@gmail.com |
Onur Sercinoglu onur.sercinoglu@marmara.edu.tr |
Pemra Ozbek Sarica pemra.ozbek@marmara.edu.tr |
How to cite:
Rasim Murat Aydınkal, Onur Serçinoğlu, Pemra Ozbek, ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism, Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019, Pages W471–W476, doi: 10.1093/nar/gkz390.
Nodes
Number of nodes in the constructed network, which is equivalent to the number of residues in the structure.
Edges
Number of edges in the network.
Average Degree
It is the average degree of all the nodes in the network. Individual degrees of all residues are also available. The values can be chosen to be sorted by residue or value, where txt. download option of the values is also available. Alternatively the hub residues can be shown on the structure or the values can be plotted to be examined in more detail.
Average Path Length
It is the average of the shortest paths between all node pairs in the network. It is defined as the average number of steps along the shortest paths for all possible pairs of network nodes. It is a measure of efficiency of information or mass transport on a network.
Density
Density of the network is defined as a ratio of the number of edges (E) to the number of possible edges in a network within N nodes.
Clustering Coefficient
Clustering coefficient of the network is a critical metric for describing the characteristic structure of a protein. Individual clustering coefficients of all residues are also available. The values can be chosen to be sorted by residue or value, where xlsx. download option of the values is also available. The values can also be plotted to be examined in more detail.
Residue Mode
When this mode is ‘ON’, residue properties (residue number and type, b-factor, eccentricity, clustering coefficient, degree and betweenness properties) are shown on the 3D structure panel and the chosen residue is also highlighted on the network.
Distance Calculation
When this mode is ‘ON’, distance between any two selected residues is calculated and shown on the structure. The chosen residues are also highlighted in the network view.
Neighboring residues
When this mode is ‘ON’, the neighboring residues of a selected node can easily be identified. The neighbors are highlighted in the network view and are also shown on the 3D structure. The node is shown in red and the neighboring residues are shown in purple.
Uniprot Annotations
This unique feature displays the natural variant and disease mutations data taken from Uniprot for the given PDB. The annotations are shown on the 3D protein structure and the details are listed on the screen.
Comparison
Comparison section enables the users to compare and visualize certain metrics (b-factor, conservation data, degree, closeness centrality and betweenness centrality) on the structures. When ‘compare metrics’ is clicked, a new window appears. There are two drop-down menus available for the user. 3D structure of the protein is colored according to the choice of the user.
3D Structure Coloring
Structure coloring based on chain, secondary structure, b-factor (taken from PDB), conservation scores and network metrics (degree, closeness centrality and betweenness centrality) is possible.
Edge Coloring
Edges are colored on the 3D structure according to the users' choices.
Shortest Path Algorithm
Shortest path between two vertices is the path that has the minimum sum of edge weights. The user can display the shortest path(s) by choosing the residues of interest from the drop-down menu. Additionally, ProSNEx offers 3 different shortest path algorithms (Dijkstra, Floyd-Warshall and Bellman-Ford) for the users, which can also be chosen from the drop down menu.
Edge Weight
For the chosen network construction type, edge weights are calculated accordingly. For any 2 chosen residues, value of the edge weight is displayed and these residues are highlighted on the network view panel.
Scatter Plot Matrix
This highly informative scatter plot matrix displays scatter plots of all the network metrics and parameters (degree, betweenness, closeness, clustering coefficient, conservation scores, b-factor and fluctuation) against each other. Data regarding the value of each can also be downloaded in a .txt and .xlsx formats.
Contact Map
Contact map is a display of the network in a 2D matrix view. Each dot represents an edge between the ith and jth residues. 2D representation of the matrix is available for download in both .txt data format and .png formats. When a cell is chosen in the distance matrix, it is also highlighted both on the 3D structure and the network view in order to ease the analysis for the user.
Distance Map
Displays the distance map between the amino acid residues. It is a matrix of elements representing the distances between any two residues. 2D representation of the matrix is available for download in both .txt data format and .png formats.
Degree Centrality
Degree is the measure of the direct neighbors of a node. The values can be listed, the list can be downloaded in .txt and .xlsx formats. When a certain residue is clicked in the list, it is also shown on the 3D structure. In the network panel, nodes are also colored and sized according to the degree values. A plot option for the degree results is also available for analysis.
Betweenness Centrality
Degree is the measure of the direct neighbors of a node. The values can be listed, the list can be downloaded in .txt and .xlsx formats. When a certain residue is clicked in the list, it is also shown on the 3D structure. In the network panel, nodes are also colored and sized according to the degree values. A plot option for the degree results is also available for analysis.
Closeness Centrality
Closeness centrality is the inverse of the total shortest path distance of the node to all other nodes of the network. The values can be listed, the list can be downloaded in .txt and .xlsx formats. When a certain residue is clicked in the list, it is also shown by in the 3D structure by zooming. In the network panel, nodes are also colored and sized according to the degree values. A plot option is also available for analysis.
Download Network
This button enables the users to download the network constructed by ProSNEx in a .JSON format.
Reset Styles
All the style changes will go back to the original view.
Reset Styles
All the style changes will go back to the original view.
Reset Styles
All the style changes will go back to the original view.
Reset Styles
All the style changes will go back to the original view.
Alternative shortest paths will be listed when clicked.
Fit to Structure
Zooms out the 3D structure and resets the view.
k-clique
k-clique defines the sub-network of k nodes with all the k nodes connected to each other. The size of the k can be entered by the user. The resulting k-cliques will be listed and the selected one will be highlighted in both the 3D protein structure and the network view.
gRINN
A tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.
Nucleic Acids Res. 2018 Jul 2;46(W1):W554-W562.
doi: 10.1093/nar/gky381
You can upload "energies_intEnMeanTotalList.dat" file obtained from gRINN.
About Data Format
About Data Format
About PDB Format
Notice
Since ProSNEx does not save the results on the server, the user is required to restart the analysis in case of closing the window.
Diameter
The diameter refers to the maximum distance between any two pair of nodes in a network. In other words, the maximum eccentricity is equal to diameter. Generally, the vertex with higher eccentricity values is located at the sides of the graph; while the nodes with low
eccentricity are the most central vertices in the graph.
Radius
The radius of a graph refers to the minimum eccentricity value.
Upload Conservation Scores
As an option, user can upload custom sequence conservation data for each chain individually. The file format should be identical to "consurf.grades" obtained from ConSurf-DB.
Eccentricity
The eccentricity of a node in a graph is considered to be the maximum distance from ni to other vertices. The minimum eccentricity refers to the radius of a network. The maximum eccentricity refers to the diameter of a network.
Threshold
The user can choose the threshold value, where the default values are specified as 7Å for C-alpha and C-beta and 5 Å for atom-pair contact networks. In the case of a low threshold value, fewer interactions will be present within that specified range leading to less edge formation. In the case of a higher threshold value, more interactions will be present resulting in a crowded network with many edges.
Carbon Alpha Network
C-alpha atoms of each amino acid are assigned as nodes. Edges are constructed between a pair of C-alpha atoms based on the threshold chosen by the user, where the default value is 7Å.
Chain of the protein.
Residue length of the chain.
If desired, the user can select sub-portion(s) of the protein by typing the desired residues. Format of selection from an individual chain is such: 10,20;35,40
Carbon Beta Network
C-beta atoms of each amino acid are assigned as nodes. Edges are constructed between a pair of C-beta atoms based on the threshold chosen by the user, where the default value is 7Å.
Atom-Pair Network
This network representation provides analysis of protein structure at the atomic level by capturing interactions between any pair of atoms based on the users’ threshold choice. The default value of the threshold is 5Å.
Interaction Strength Network
Edges between nodes are added only if the interaction strength is more than the user-specified threshold, where the default value is 4%.
Interaction strengths as edge weights
The interaction strength values are taken from Kannan et al.
This option is only available when Interaction strength is chosen to construct the network.
Upload New Molecule
By clicking on this button, the user can upload a new molecule.
This option is ‘ON’ as default. The user can change it to hide the secondary structure.
This option is ‘ON’ as default. The user can change it to hide the network shown on the 3D structure.
This button enables the users to display the chosen residue both on the 3D structure of the molecule and the residue interaction network panels.
Edge Weights from gRINN
The tool provides the option of using Interaction Energy Matrices (IEM) given by gRINN to construct a network.
Edge Weights from gRINN
The tool provides the option of using Interaction Energy Matrices (IEM) given by gRINN to construct a network.
NMA Cross-Correlations from PDBj
This option provides the usage of Normal Mode Analysis (NMA) information found in PDBj database for the construction of a network.
This option is only available upon individual chain selection or when the whole structure is chosen.
NMA Cross-Correlations from ANM/GNM
Cross-correlations from Anisotropic Network Model (ANM) or Gaussian Network Model (GNM) are used as edge weight.
Network Type
User's choice of network type and cutoff value is displayed.
Edge Type
User's choice of edge type is displayed.
Export Network View
Screenshot of the displayed network can be exported in jpeg format.
Network Layout
Different network layout options can be reached using this drop-down menu.
Cross Correlations Map
Displays the cross correlations map obtained from Normal Mode Analysis (NMA). This option is present only when a weighted network is constructed using ANM, GNM or PDBj options.
Square Fluctuations
Displays the square fluctuations obtained from Normal Mode Analysis (NMA). This option is present only when a weighted network is constructed using ANM, GNM or PDBj options.
Sequence Conservation Scores
Displays the conservation scores of each residue obtained either from ConSurf-DB or user uploaded data.
B-factors
Displays b-factors obtained from PDB.
Start a new project
For new tasks, users should choose this option.
Import workspace
Users can choose this option to upload their previously saved .prosnex workspace.
Normalize
Normalizes the value between 0 and 1.
Multiple Pairs
Multiple source-target entries can be provided in each line to display the shortest paths among these pairs