Input:
Input for PDB scale:
First, the protein and RNA structures that you want to predict must be provided by the following two ways:
1. Provide a PDB id. If you provide structure by this way, the webserver will fetch the structure from PDB.
2. Upload a file.
Second, the chain id must be assigned.
Input for genome scale:
First, the protein and RNA structures that you want to predict must be provided by the following way:
1. For protein, you can provide a PDB id, then the webserver will fetch the structure from PDB. Besides, you can upload a file.
2. For RNA, you must provide the 2D structure of RNA, such as 2D structure exampleThe secondary structure state ends with "#FS".
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Output:
Output for PDB scale:
*ResultOut, it's a result file sorted by 3D2Dscore. The higher the ranking, the target structure and the template structure are the more similar. Each column represents: template ID, TMScore, RNAsimilarity 3D2DScore, 5-9 and 10-14 columns are TP, FP, TN, FN and N for protein and RNA binding sites prediction, respectively.
PRIME_out, it's a result file including the sequence and the predicted binding sites, in which ‘+’ indicates prediction as a binding site, '-' is predicted as a non-binding site, and ' ' indicates that residues/bases cannot be aligned between target and template.
PRIME_err, it's the error file including error message.
Output for genome scale:
*resultout, it's a result file sorted by 3D2Dscore. The higher the ranking, the target structure and the template structure are the more similar. 1-4 columns represent template ID, TMScore, RNAsimilarity, 3D2DScore. If the binding sites of target RNA are provided, then 5-9 columns are represent TP, FP, TN, FN and N for RNA binding sites prediction.
PRIME_out, it's a result file including the sequence and the predicted binding sites, in which ‘+’ indicates prediction as a binding site, '-' is predicted as a non-binding site, and ' ' indicates that residues/bases cannot be aligned between target and template.
PRIME_err, it's the error file including error message.
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