To aid the creation of PDB and ConSurf files for the DR_bind server you can use the following form and enter the PDB ID and Chain ID or upload a PDB file and submit them for preparation.
You will be directed to a webpage where you can download the cleaned PDB file and to a link to the output from ConSurf. When ConSurf has finished you will need to download the Amino Acid Conservation Scores, Confidence Intervals and Conservation Colors file. Both the PDB file and the consurf.grades file can then be used in option A for the DR_bind server.
In the event that ConSurf data can not be generated it is possible to still obtain a prediction, please look at the help pages for information.
In this guide, we provide an example of how to obtain the evolutionary data of your target structure by listing the options provided by the ConSurf server and providing you with suitable selections of those options.
However while we offer suggestions to the ConSurf options you are still free to change any parameters based on your own case.
|
Step
|
The options provided
by ConSurf
|
Suggested selection
for the user
|
Notes on the options
|
|
1
|
Analyze Nucleotides or Amino Acids? | Amino-Acids | |
|
2
|
Is there a known protein structure? | YES | You need to either enter
the PDB ID code or upload your own PDB file. Then the
corresponding chain identifier is required. |
|
3
|
Do you have a Multiple Sequence Alignment (MSA) to upload? | YES (If there is any) | Option to allow you to upload your Multiple Sequence Alignment file or Tree file. |
| NO (If there is none) | This is most likely option
in most cases. |
||
|
4
|
Choose parameters to build the Multiple Sequence Alignment (MSA) | Option to allow you to choose parameters for generating the multiple sequence alignment or in most cases use the default values. | |
|
5
|
Press the Submit button and enter your e-mail address to receive a mail of predicted results. | ||
|
6
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ConSurf jobs running | Waiting... XD | |
|
7
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ConSurf jobs finished | When the jobs was finished, please click on the file "Amino Acid Conservation Scores, Confidence Intervals and Conservation Colors", save it and upload it to our server | |