PROXiMATE Database

TUTORIAL: USING THE SEARCH FORM AND UPLOADING DATA

ADVANCED SEARCH

The Search form can be used to search for entries of your interest. There are two sections: a Build Search Query table (to specify a search query) and a Display Columns table (to choose columns to display). All fields are optional. However, leaving all fields default will not provide any result. Please provide a query in at least one field in the search form. Multiple queries will be processed using AND logic (for example, if the user specifies a PDB ID "1CBW" and mutant K_D value of 1.00e-9 in the From field, then the search will retrieve entries for which both conditions are true). The Reset button will refresh the search form to display default options.

The Build Search Query table to specify the search query

Protein Complex:

This consists of two search fields and can be used to search for a particular protein or a protein complex by name. For example, if you would like to retrieve all complexes containing barnase, select "Bacillus amyloliquefaciens barnase/ribonuclease" from the protein 1 drop-down box. If this box is filled, the second box will provide a list of proteins which interact with protein 1 ("Bacillus amyloliquefaciens barstar") and have known mutants with associated thermodynamic data deposited in PROXiMATE.

PDB ID:

Enter the PDB ID of the protein-protein complex. This field is case-insensitive (for example, typing either "1CBW" or "1cbw" will provide the same result.)

Residue Mutation:

Two fields are provided. The first is used to specify a wild-type residue, and the second for the mutated residue. The results can include both single and multiple mutations. All chains are searched for the mutation specified by the user.

Secondary Structure:

Users can search for a specific secondary structure assigned by DSSP at the mutated position using the drop-down list.

Functional Class:

Users can search for complexes by a particular functional class. These are provided in a drop-down list.

Class	Description
Any Class	Default option (no class specified)
Ag-Ab	Antigen-antibody complexes
EI	Enzyme-inhibitor complexes
GC	G-protein containing complexes
HR	Hormone receptor complexes
OE	Other enzyme-containing complexes (i.e. protein interacting with the enzyme is not a known inhibitor)
RC	Receptor containing complexes (i.e. protein interacting with the receptor is not designated as a hormone)

Experimental technique:

Users can search using any experimental technique. Please note that, due to the diversity of terms that may be used to refer to the same experimental technique, searching by a particular technique may not provide complete results. Wherever possible, we have tried to maintain a standard nomenclature. However, in some cases, the technique was not be mentioned, or the description was too vague to deduce the correct name for the technique used to obtain the data.

Author:

Users can also search by author's name. This is case-insensitive and can match partial queries with the author's name, but it will not match wrong spellings. For example, the search query "gold" will match all entries with the author "Goldman", but "gild" will not match the same. This search field will not be able to handle special characters (like accent marks).

Wild-type Kd (M), Mutant Kd (M), ΔΔG (kcal/mol), Wild-type ΔG (kcal/mol), Relative Accessibility:

Users can also search for a particular range of values in each of these parameters. The From field must contain the lower limit and the To field must contain the upper limit. If the To field is left blank, the search will include all entries with values greater than or equal to the lower limit. If the From field is left blank, all entries with values less than or equal to the upper limit will be retrieved. If the From and To fields are equal, entries which exactly match the given value will be retrieved.

Year:

Two fields are provided, From and To, to specify the lower and upper limit respectively. For example, 1997 to 2010 will retrieve entries for which the reference publications were published between 1997 and 2010 (including both years). If both fields are equal, all data published in that year will be retrieved. If the To field is left blank, all data published from the specified year (including the most recent data) will be presented. If the From field is left blank, all data published published upto the specified year will be retrieved.

Display Columns:

Use this table to specify which columns to display in the search results page. Some columns are selected by default. The number of results to be displayed per page can also be selected.

The Display Columns table to select columns to be displayed in the search results

SEARCH FOR ENTRIES WITH MUTATIONS FROM ISOLEUCINE TO ARGININE

To search for Ile(I) to Arg(R) entries, navigate to the search form.
In the Build Search Query table, go to the 3rd row (Residue mutation from).
Select I (Ile) in the first dropdown box and R (Arg) in the second box, as shown.

How to search for Ile to Arg mutations

Check the columns you wish to display, and the number of results to be shown on each page. Click the Submit button.
You will be directed to a Results Display page. You can download all the results, or explore individual entries further by clicking on the Entry number.

Search Results for entries containing Ile to Arg mutations

SEARCH FOR BARNASE-BARSTAR PROTEIN COMPLEX

To search for a specific complex, navigate to the search form.
In the Build Search Query table, go to the 1st row (Protein Complex).
In the first dropdown box, select "Bacillus amyloliquefaciens barnase/ribonuclease".

How to search for a specific complex: barnase-barstar

The second box will automatically choose the interacting partner, barstar.

Protein 2 box is automatically populated

Check the columns you wish to display, and choose Results per page as 50. Click the Submit button.

Adjust the number of search results per page

You will be directed to a Results Display page. You can download all the results, or explore individual entries further by clicking on the Entry number.
Click the tabs 1, 2, 3 to see each results page.

Search Results for barnase-barstar complex

SEARCH FOR A RANGE OF ΔΔG VALUES

ΔΔG refers to the difference in binding free energy change between the mutant and the wild-type. The formula used here is

ΔΔG = ΔG_mut - ΔG_wt

where mut = mutant and wt = wild-type.

To search for a range of ΔΔG values, navigate to the search form.
In the Build Search Query table, go to the 11th row, third from the last row (ΔΔG values in kcal/mol).
Provide the lower limit (-3.0) in the first box, and the upper limit (-1.5) in the second box.

How to search for a range of ΔΔG values

Check the columns you wish to display, and choose Results per page as 50. Click the Submit button.

Adjust the number of search results per page

You will be directed to a Results Display page. You can download all the results, or explore individual entries further by clicking on the Entry number.
Click the tabs 1, 2, 3 to see each results page.

Search results for ΔΔG value range

HOW TO UPLOAD YOUR DATA

Authors can share published data on thermodynamics and kinetics of mutant protein-protein complexes for inclusion in the database. The upload form has been created to enable authors to share the data. In this section, we will provide a short tutorial on how to upload your data for sharing.

The upload form for sharing data

The upload form consists of two sections, in which all fields are mandatory, except for the complex PDB ID. The first section is for communicating with the author, should the need arise. Please note that your personal details, including email IDs, are considered confidential and will never be shared with third parties.

The second section contains input fields for data which may be ultimately included in the database. Therefore, we request the author to ensure accuracy. Please adhere to the following guidelines for data submission.

Please ensure that the data to be shared has been published and the reference publication indexed on PubMed.
While the PDB ID field is not mandatory (as all complexes may not have experimentally determined crystal structure), we strongly recommend providing a PDB ID for DSSP calculations.
Please provide standard protein names, as found in UniProt. It will be helpful if you can provide the UniProt accession ID in brackets.
The experimental technique can be expressed in a short phrase of 2 - 5 words, such as 'Surface Plasmon Resonance' or 'Competitive Inhibition'.
Please indicate the ionic conditions used, for example, '25mM CaCl2,150mM NaCl'.
We request that the temperature be specified in units of Kelvin.
The pH field may be filled with a decimal value in the range 0.0 to 14.0.
We have provided a text box for submitters to copy and paste their data from a spreadsheet or .txt files. Please ensure that the data meets the following criteria:

Data in tabular format as shown below.
The mutation, in the format ch:wt-pos-mut or wt-mos-mut if chain is not known.
Appropriate notation and units. For example, if you are submitting the K_D values, please use scientific notation ('3.4e-9') in Molar (M) units.
Column names to identify the type of data. For example, Kd for binding affinity, kon for association rate, ddG for binding free energy change.
The corresponding wild-type data in a separate row, for the same experimental conditions.

All data submissions are subject to verification and redundancy checks.

Filled-out example for data entry text area

Please see the FAQs for a description of the notations and units used. We request the submitter to provide all data values in the standard units used in PROXiMATE. Mutant data for association and dissociation rates, dissociation constants, free energy of binding, enthalpy and entropy can be provided. Please provide the corresponding wild-type data as well. Multiple substitution mutations on both sides of the interface can be included.