Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

This parameter controls the frame sampling rate from the MD trajectory. A larger number will result in faster calculations at the expense of accuracy.

These options are a variety of network centrality metrics that can be applied to a representation of a single protein structure. Network centrality are different ways of investigating node importance in a network. As they are computed from a single structure, they are not averaged.

This is the cut-off distance in Angstroms used to infer residue contacts. We recommend the default value of 6.7 Angstroms. While smaller or larger values may work in simpler calculations such as DC, convergence problems may be experienced for very different values for metrics based on shortest path calculations and those using matrix factorization, such as EC. Larger cut-off values will also increase computation time, as more edges need to be traversed. DRN statistic

Three options are provided as summary statistics for residue centralities computed across each frame, namely the average, median and standard deviation.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure. Compared to DRN calculations, the computation of a residue interaction network (RIN) from a single structure is much faster. However, one should take into account that proteins are inherently dynamic. From our experience, we observed that RIN was influenced by criteria of energy minimisation, for e.g. related samples would not cluster together when the number of EM steps is changed. Step

This parameter controls the frame sampling rate from the MD trajectory. A larger number will result in faster calculations at the expense of accuracy.

These options are a variety of network centrality metrics that can be applied to a representation of a single protein structure. Network centrality are different ways of investigating node importance in a network. As they are computed from a single structure, they are not averaged.

This is the cut-off distance in Angstroms used to infer residue contacts. We recommend the default value of 6.7 Angstroms. While smaller or larger values may work in simpler calculations such as DC, convergence problems may be experienced for very different values for metrics based on shortest path calculations and those using matrix factorization, such as EC. Larger cut-off values will also increase computation time, as more edges need to be traversed

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. This computation is based on C-beta and GLY C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

A residue is specified by both its 3-letter code and its position in the topology file according to the residue name and number sections. The chain of interest is also specified according to the relevant field in the tpology file.

This is the cut-off distance in Angstroms used to infer residue contacts. A larger number will result in faster calculations at the expense of accuracy.

This parameter controls the frame sampling rate from the MD trajectory. A larger number will result in faster calculations at the expense of accuracy.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

This tool aggregates the contacts predicted from various related contact map calculations and represents them as a heat map. The files can be selected from Select, which contains a list of previously completed contact map calculation jobs. It is important to properly name the contact map job files such that these can be unambiguously located from the list. Local CSV files can also be specified via the Upload option.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

This parameter controls the frame sampling rate from the MD trajectory. A larger number will result in faster calculations at the expense of accuracy.

Comma-separated list of unique atom names (without spaces) which will be selected for DCC calculation (e.g. 'CA,P'). The backbone phosphorus 'P' atom can be a good choice for representing nucleotides.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Please ensure that no non-protein atom labeled as "CA" is present in your data. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

This parameter controls the frame sampling rate from the MD trajectory. A larger number will result in faster calculations at the expense of accuracy.

This represents the number of minute random uniformly distributed forces applied to each CA atom to drive overall motions. Each residue is scanned with this approach. By comparing the similarity of the perturbed conformations to that of a desired conformation, one can determine hotspot residues that drive conformational changes associated with some defined state.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The complex refers to a the PDB-formatted file of a protein.

This parameter controls the number of atoms to be retained from the provided PDB file, which will be used later on to calculate the anisotropic network model. Higher CG values increase amount of coarse graining, leading to fewer residues. This value is generally increased when working with large proteins, as it decreases memory and time required for the computation.

Choose CA or CB to select alpha or beta carbon atoms (with CA for the GLY residue), respectively.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The protein structure can be a previously coarse-grained protein in the "Coarse Graining" step, or one that has not been goarse-grained.

The cut-off distance in Angstroms is used to infer residue contacts. A larger number will retain more atoms for the calculation of the ANM model. Smaller cut-off values may result in too sparse and inaccurate protein representations. A reasonable value will be partly informed by the presence of six leading eigenvalues associated to the resulting normal modes.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The previously coarse-grained protein used to build the anisotropic network model.

These are the data sets "W_values.txt" and "VT_values.txt" obtained from the previous ANM construction step, which contain the frequencies and their corresponding modes.

Choose CA or CB to select alpha or beta carbon atoms (with CA for the GLY residue), respectively. This should correspond to the atom type used for building the ANM model.

Specify a range of modes in the format M1:M2. For example, to calculate MSF over the first 20 non-zero modes enter "7:27". To calculate the MSF from a specific combination of modes, enter the mode numbers separated by a comma, for e.g. "1,5,7"

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

The mode number to visualise

By ignoring a certain number of residues at the termini, the performance of decomposition can be improved. Independent analysis of RMSF may assist in setting these parameters. From our observations, this generally affects the last 2-3 residues of the C-termini. The removal is applied the same way to each chain of a complex.

Generate a multi-PDB file showing the effect of the mode on the protein.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

If another topology and trajectory pair is provided, the tool will perform comparative essential dynamics. One important requirement is that the data used should be comparable (same number of alpha carbon atoms and number of MD frames)

Perform ED using the specified selection (MDTraj selection syntax) Only CA atoms will be selected from the selection. It is thus most applicable when specifying residue(s) and/or chain ID(s). Selection is performed after having done a global fitting of the entire structure.

Selection examples:

Select residues 1-10: 'residue 1 to 10'

Select the first chain: 'chainid 0'

Select the residues from 1st and second chains: 'chainid 0 and (residue 10)'

This parameter controls the frame sampling rate from the MD trajectory. A larger number will result in faster calculations at the expense of accuracy.

Expected number of clusters for automated conformation extraction using k-means clustering. This has no impact on the essential dynamics - only on the predicted possible equilibrium conformations. This algorithm is used alongside another one which already finds the conformation of maximal probability density.

By ignoring a certain number of residues at the termini, the performance of decomposition can be improved. Independent analysis of RMSF may assist in setting these parameters. From our observations, this generally affects the last 2-3 residues of the C-termini. The removal is applied the same way to each chain of a complex. Sometimes these changes may be relevant - knowledge about the protein always helps.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

For an example of what to expect, and its interpretation click the View demo button below

Click on the button on the left for an introduction of the tool. Hover on the input sections for hints.

The topology file is usually the viewable structure that has a matching trajectory. As the computation is based in C-alpha (CA) atoms, it is more efficient to use a topology and trajectory file that only contain these atoms. Choose the Upload option from each cyan box to upload files that are from your local machine. Previously uploaded topology and trajectory files can otherwise be specified using the Select options. The trajectory can also be remotely uploaded from the provided URLs.

This parameter controls the frame sampling rate from the MD trajectory. A larger number will result in faster calculations at the expense of accuracy. This number should not go beyond the number of frames.

For an example of what to expect, and its interpretation click the View demo button below