MetalS3 help

This section explains the web user interface of MetalS3 and acts as a reference for experience users, novice, and anyone in between. This page will help you to find your way around MetalS3.

Introduction

MetalS3 is a database searching tool aimed in identifing structural analogs for a given query structure of Minimal Functional Site (MFS). The MetalPDB database used as the target database for searching because MetalPDB provides a well-maintained clusterization of the MFSs structures. Thank to this clusterization a large number of structures is divided into groups of similar MFSs thereby eliminating the need of performing redundant comparisons. Still availability of different levels of search allows drilling down into the specific groups of structures which users are interested in.

How can I specify my query structure

This form allows you to specify the query structure.

(1) The query structure can be defined by passing a 4-letters PDB code into the PDB code field.
(2) As an alternative, you can browse your local hard drive using the Browse button and upload the PDB-file of a structure containing MFS.
(3) Change the default value of 2.8 Å in the Threshold coordination distance field to control the distance between metal atoms and donor atoms when MFS is extracted from PDB.
(4) Adjust the default list of atoms in the Excluded donor atoms field entering the chemical symbol(s) of the atom(s) (separated by commas). Specified atoms will not be identified as atoms that coordinate the metals, thus, will not be considered as donor atoms.
(5) Enter the chemical symbol(s) of a specific metal(s) into the Metal of interest (optional) field to extract MFSs that inclued specified metals. The MFS will be only done near atoms of this type.
(6) Click Search for Sites to examine the query structure for MFSs.

How can I specify MFS

All detected MFSs are listed.

(7) Review the list and select one for further comparison against the MFSs in the MetalPDB.
(8) Click Create Job to proceed to the page where you can set and submit the search job.

How I can set and submit a MetalS3 search job

MetalS3 works with a set of job options that allow a user to adopt the search job to perform a more specific task. Hit Submit Job to run search with default parameters or customize the settings described below.

(9) MetalS3 supports two types of search that the you can choose. The first one is structural search containing structures TBD; the second one is functional search containing structures TBD.
Using the metals filter (10) allows you adjusting searching set content before processing. Using this filter you can restrict searching set to be populated by MFSs structures having particular metals. This can speed up the search substantially as it reduces a number of structures over which you perform the comparison.
(11) The distance of matching affects the limit of the distance between two atoms in order to consider these atoms as matched to each other.
(12) With the quality threshold less then 100% you may lose the best alignment for the sake of saving time spent on waiting search results.
MetalS3 may also imply filters after processing. In that case filtering affects only the reported data.
(13) The set of thresholds may be applied to all components of the score. The values of components in resulting report will not exceed specified thresholds.
(14) Filtering by percentage of equivalent residues enables users to remove from results cases having a value of percentage outside of the specified range. The percentage is calculated over aligned region by comparing the number of pairs of equivalent residues to the total number of pairs in alignment. Ranges are inclusive.

(15) You may optionally specify a job name. The job name appears in the Subject field of the email notification.
(16) A valid email address is required. The server sends an email notification to this address when the job has finished.
(17) Review set parameters and hit Submit Job to start the search.

Place your mouse over an image like this one to obtain a brief help on the "tooltip".

Review MetalS3 search results
When the searching process is completed, the server provides the user an access to a web page with results. The resulting web page displays a list of records and looks like the one below.
Each record contains site ID (18), information about metals (19) and ligands (20), a value of RMSD (21), values of separate terms of a scoring function: geometric (22), size (23), chemical (24), the total score (25) obtained as a result of comparison, and the percentage of equivalent residues (26).
The 3D superimposition can be visualized in a pop up window and displays the selected structure superimposed on the query structure. Hit the icon (27) to visualize alignment.
A Jmol applet is used as structure viewer. The applet requires Java Run-time Environment (JRE) installed on your local machine. You can download the latest Java at java.com.
Moreover it is possible to examine a sequence alignment based on structural alignment for each comparison. Hit the icon (28) to view sequence in a pop up window.
You can select (29) any of listed MFS for further analysis.
You can notice a small button (30) at the right top of results page. Hitting the button will pop up a window allowing on-the-fly filtering of search results.
As you type into it, any results with values that don't meet at least one of the specified conditions will be filtered out. Hit Apply to let the filter affect the resulting page.
At the bottom of the table with results you can see a record telling you what is the total number of results, the total number of results after filtering has been applied, and the nubmer of results are displayed.
The results can be downloaded as a CSV file (33) and stored locally for the further processing.