How to use
1. Input files you should provide
Before making a prediction using MetalExplorer, several input files should be provided by the user, which include:
(1) PDB file (.pdb), which can be downloaded from the RCSB Protein Data Bank;
(2) A sequence file in the FASTA format of the PDB chain you want to predict (.fasta). Please make sure that this file ONLY contains the fasta format sequence of the chain you want to predict. This file can be obtained from the RCSB Protein Data Bank;
2. How to submit your job and check prediction results
Once these input files are ready, submitting your job to MetalExplorer is easy and straightforward.
(1) Although the task name is optional, it is mandatory to provide your Email address since the prediction results will be sent to you by Email.
(2) Meanwhile, please designate the type of metal ion and the PDB chain ID that you would like to predict. An example is given as follows.
(3) When all input files are ready, click the "Submit" button to submit your job. You can also reset your input by clicking the "Reset" button.
(4) After job submission, you will be redirected to a notification webpage providing your job ID and a URL linking to the result webpage. Please do NOT refresh the notification webpage because this will lead to multiple submissions!!!
(5) The following is the result webpage. It has three sections- job summary, line chart of the prediction scores and detailed prediction results as per residue.
(6) Due to the complexity of PDB files, there can be some exceptions of which no valid prediction outputs are generated. Thus, in cases where you have been waiting for more than one hour after the submission and no results have been returned, feel free to contact us (Chen.Li@monash.edu) by sending your input files and job ID. We will manually check and process these files for you.