Elhabashy Lab

Here you can upload your cross-linking mass spectrometry data in a comma separated value file (.csv). This file is required to contain 8 columns named: "peptide1", "peptide2", "position1", "position2", "k_pos1", "k_pos2", "entry1", "entry2".

peptide1 and peptide2: Peptide sequences

position1 and position2: Starting positions of the corresponding peptide in protein sequence

k_pos1 and k_pos2: Position of the linked residue in the corresponding peptide

entry1 and entry2: UniProtID for corresponding protein.

You can leave the columns k_pos1 and k_pos2 empty if you do not have the information available, since they are only used if the peptide positions provided do not match the retrieved UniProt sequence and need to be validated.

Optionally you can enter a name for job, which can be used in the job search, if you loose the assigned jobID.

The cross-linker parameters are used in the structural analysis to compute distances between cross-linked residues. They depend on the used cross-linker.

The linker minimum and linker maximum range are the lower and the upper limit that should be considered valid for the used cross-linker. Their default values are 5.0 and 35.0.

Cross-linking residues can be used to specify which residues the cross-linker binds to. It should be a comma-separated list of one-letter coded amino acids. Optionally you might add two colon-symbols, if you wish to specify the position of the residue in the sequence and/or the atom in the residue used for the distance computation.

After the first colon-symbol you can place the atom type for the distance computation (allowed: "N", "CA", "C", "O", "CB"). If no value is set here 'CB' will be used by default.

After the second colon-symbol you can place one of three position values: 0 if the residue may occur anywhere in the protein, 1 if the residue has to be at the N-terminus, or -1 if the residue has to be at the C-terminus

ex.: use "K:CB:0" to calculate the cross-link distance between lysin C-beta-atoms at any position in the chain.

If you want to specify multiple possible positions for the same symbol you have to add them individually (ex.: "M::1,M::-1" for methionine at either the beginning or end of the chain). By default, 0 is set here, e.g. the residue may be placed anywhere.

Note: If the position or the atom type is specified there have to be two colon-symbols (ex.: "K,M:1" will not be accepted as input). you can leave the respective specification empty though, if you wish to use the default here (ex.: "K::1" is equal to "K:CB:1", "M:N:0" is equal to "M:N:", "K:CB:0" is equal to "K::" and also to just "K").

Default: "K,M:N:1" for Disuccinimidyl suberate (DSS) linker

The e-value, query identity and coverage can be used to control the search query used to find structures from RCSB-PDB.

The e-value describes the probability of finding this match by random, it is in the range of [0,1]. The default value is 0.00001.

The query identity is the percentage of the match that is identical to the query, it is in the range of [0,100]. The default values is 90.0.

The coverage is the percentage of the query that should be included in a match, it is in the range of [0,100]. The default value is 50.0.

The resolution and pLDDT cutoff are used to pose a lower limit on the quality of the 3D structures.

The resolution cutoff applies an upper limit on the structure resolution of files downloaded from the RCSB-PDB, if the used experimental method provides a resolution. The default value is 4, this parameter only accepts natural numbers.

The pLDDT is a confidence measure used in AlphaFold predicted structure models. It is called predicted local distance difference test, which can be considered as a per-residue confidence on the prediction. It ranges from 0 to 100, where values above 50 are considered very low quality, values from 50 to 70 are of low quality, values above 70 are condidered of good quality and values above 90 are of very good quality. For values above 90 usually the backbone and the side chains of a residue can be considered predicted correct, while for values above 70 the backbone can be considered correctly predicted. The default value is 70.

If the compute-scoring parameter is set to True, an inter-interaction confidence score is computed that leverages the results from the structural and the OPS analysis to give an idea on how confident CLAUDIO is with its reevaluation. It is of range [0,1], where 1 indicates the highest confidence in observing an inter-link

The parameters euclidean-strictness, distance maximum and cutoff can be used to specify the score to your needs.

The euclidean-strictness is applied to the euclidean distances computed in the structure analysis by subtracting this value from the observed distance. It needs to be greater or equal to 0, or 'None' if the euclidean distances should not be used for the final scoring (only use topological distance and OPS analysis).

The distance maximum is a maximum value the computed distance will be replaced with if it is surpassed, to provide an upper limit for the score. It can be greater or equal to 0.

The cutoff is the threshold CLAUDIO uses on the score to decide whether a cross-link is an inter-link. This happens if this threshold is surpassed. The default is 0.