GUI | gses2

Analysis	Submitted	Status	UMF	cis/len (%)	Results
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User Guide

Use this tool to compare Cα–Cα distances among multiple structural samples of the same protein and calculate the UnMorphness Factor (UMF).

Quick start

Select an input mode and enter a UniProt ID, PDB ID/chain, or upload mmCIF files.
Review the coverage, identity, analysis range, and cis-distance settings.
Select Submit Analysis. The job will appear in Analysis History.
When the status is Completed, select View to inspect and download the results.

Input modes

UniProt: Retrieves structures associated with the specified UniProt accession and the selected experimental method. Closely related accessions may be combined with a plus sign, for example P12345+Q67890.
Direct PDB Entry: Analyzes explicitly specified PDB entries or chains, for example 1ABC:A 2DEF:B. PDB entry IDs are case-insensitive; chain IDs are case-sensitive.
Upload mmCIF Files: Uses compatible protein chains from uploaded .cif or .mmcif files. Up to 20 files may be uploaded; the limits are 25 MB per file and 100 MB in total.

Analysis parameters

Experimental Method: Limits the automatic UniProt structure search to X-ray, NMR, or EM entries. Explicitly included PDB entries are added independently of this search filter.
Sequence Coverage (%): Minimum percentage of the reference sequence that must be represented by a structural sample.
Sequence Identity (%): Minimum sequence identity required when a chain is aligned to the reference sequence.
Analysis Range: Restricts the analysis to a residue range. Start = 0 and End = 0 analyze the full available length.
cis CA–CA Threshold (Å): Maximum adjacent Cα–Cα distance used by the cis analysis. The default is 3.3 Å.
Exclude chains with internal CA gaps: Removes chains containing internal missing Cα positions within the selected analysis region.
Save distance data (CSV): Retains the pairwise distance data as an additional CSV output. It is disabled by default because the file can be large.

Including and excluding PDB chains

In UniProt mode, structures entered under PDB ID / Chain to Include are added to those retrieved for the UniProt ID. For example, 7LW3:B adds chain B, whereas 7LW3 adds all compatible protein chains from that entry. Added chains must still satisfy the Sequence Identity and Sequence Coverage settings.

PDB ID / Chain to Exclude removes an entire entry, such as 7LW3, or one chain, such as 7LW3:B. If the same entry or chain is present in both fields, exclusion takes precedence.

Results

The result summary reports the number of entries and chains, analyzed length, coverage, resolution, UMF, cis frequency, and UMF rank when reference ranking data are available.

Score heatmap: residue-pair DSA scores.
Progress plot: UMF as structural samples are added.
Semi-log main plot: DSA score versus average Cα–Cα distance.
Distance standard deviation plot: distance variability versus average Cα–Cα distance.

Use Download all results (.zip) to retrieve all retained files for a completed job. Distance data are included only when the corresponding option was selected.

Analysis History

History lists submitted jobs and their status. Select View to expand a completed result, Hide to close it, or Delete to permanently remove an eligible job and its files. Administrators can view all jobs; other history visibility follows the site’s configured access scope.

New jobs show a scheduled deletion date in the expanded result and are automatically removed after the 14-day retention period.

Analysis Examples

These worked examples show how DSA can analyze corresponding protein structures without requiring global structural superposition, including a protein embedded in a large assembly and multiple models from one NMR ensemble.

Pseudomonas aeruginosa ribosomal protein uL6

Combining Q9HWF0 and A0A2V3F3S9

Q9HWF0 is the reviewed UniProt record for the P. aeruginosa large-subunit protein uL6. A0A2V3F3S9 is another P. aeruginosa uL6 record used by ribosome structures from a clinical isolate; for example, PDB 6SPB is described as a 50S ribosome from a clinical isolate with a mutation in uL6.

Entering the accessions with a plus sign pools structural samples found through both records. This is valuable when the biological target is the same conserved ribosomal protein but the relevant PDB chains are divided between a reference accession and an isolate-specific accession.

Input mode: UniProt
UniProt ID: Q9HWF0+A0A2V3F3S9
Method: EM
Coverage / identity: 90% / 95%
Range: Full length (0–0)
Internal CA gaps: Allowed

Methodological advantage: uL6 is extracted from a very large ribonucleoprotein assembly, but DSA evaluates corresponding distances within uL6 itself. The result is therefore unaffected by rigid translation or rotation of the complete 50S particle and does not require superposition of the entire ribosome.

Type II secretion system core protein G

Using the NMR ensemble for UniProt E0SM38

E0SM38 is a Type II secretion system core protein G from Dickeya dadantii. Its NMR structure contains multiple deposited models in a single PDB entry. The Web runtime expands these models into separate structural samples and applies DSA to their corresponding intramolecular distances.

This example demonstrates that one NMR ensemble can provide enough structural samples for DSA even though the History table reports only one PDB entry. In the example run shown here, 10 models were retained over 122 residues (79.7% of the UniProt sequence), giving UMF 83.4.

Input mode: UniProt
UniProt ID: E0SM38
Method: NMR
Coverage / identity: 70% / 95%
Range: Full length (0–0)
Internal CA gaps: Allowed

Methodological advantage: each NMR model may have an arbitrary rigid-body placement, but its internal Cα–Cα distances are invariant to that placement. DSA therefore characterizes distance variability across the ensemble without selecting a reference model or performing a global least-squares superposition.

Terms & Data Policy

This policy explains the acceptable use, storage, and limitations of the DSA / Cis Analysis service. By submitting an analysis, you agree to these terms.

Purpose and scope

This service is provided for academic and research use. It accepts public structure identifiers and user-supplied mmCIF structure files and produces computational analysis results.

Uploaded and unpublished structures

You may upload an unpublished structure only when you are authorized to do so. Do not upload data covered by an NDA, patent-related restriction, clinical confidentiality requirement, export restriction, or any other obligation requiring stronger protection than this policy provides.

The service is not an archival repository or a system designed to provide NDA-grade confidentiality. For highly confidential data, contact the laboratory to arrange an appropriate method before transferring any files.

Storage, access, and automatic deletion

Each new job—including uploaded inputs, derived results, and logs—is scheduled for automatic deletion 14 days after submission.
Deletion is performed when the analysis worker next runs, so it may occur shortly after the stated expiry time rather than at that exact minute.
Users should download required results promptly. Continued availability and recovery after deletion are not guaranteed.
History visibility is separated using the observed IP address and a browser identifier. This is convenient separation, not user-account authentication.
Site administrators may access jobs when reasonably necessary for operation, maintenance, security, or troubleshooting.

Use of submitted data

Submitted structures and derived results will not be used by the service operator for independent research, publication, redistribution, or AI training without separate permission from the submitter. Routine automated processing and administrator access needed to operate or troubleshoot the service are not considered secondary research use.

Scientific use and publication

You may use downloaded results in research and publications. You are responsible for validating the input data, computational results, statistical interpretation, and scientific conclusions. Please cite the DSA method and any relevant external databases or software used by the analysis.

Availability and disclaimer

The service and its results are provided on an “as is” and “as available” basis for research use. Analyses may fail, contain errors, or become unavailable, and data may be lost because of maintenance, software defects, network problems, or other operational events. Nothing in these terms excludes or limits liability where exclusion or limitation is prohibited by applicable law.