Structure Only Submission: You are allowed to submit upto 10 PDB files to the server at a time. During submission each of these files are checked for correctness. The PDB files require to have SEQRES records in them. If you do not have any, get one and paste it on top of your PDB file. Only text files are accepted.

If you have FSSP files for your PDBs please upload them or else the server will not use the fold information during calculations. Also, input the taxa code for the species to which your protein belongs. During analysis of alignments, taxa information helps discriminate closely related sequences.

Sequence Only Submission: You are allowed to upload Sequence information in three modes. (i). You enter one file with all information in FASTA format. The webserver will parse your sequence information and produce it for you to validate and submit. The first word in your FASTA sequence header is used as a key (job ID) to submit jobs. So if you have these headers unique it may help you to keep a better job inventory. In the second mode (ii), you are allowed to paste in the text box, further to which the websever parses your input and makes individual job submissions. The first word of the header information is used to create a job ID and it might help to keep that unique for better job inventory at your end. The third mode (iii) allows you to upload individual files for 1 sequence in FASTA format. The names of the files uploaded are used to create the job ID and returned to you by email.

All the submit modes have some restrictions to the number of jobs that can be submitted at a time. Please use the queues sensibly and not BATCH submit large number of jobs by repeatedly using the page at a time. Currently, there is no restriction to the number of times you can batch submit. It would be appropriate to submit the next batch once your first batch has completed and you have received emails. Please include a valid email ID for returning your job results. Also include a NCBI species code for all the sequences, where ever possible. You can follow up on the progression of your jobs online through the progress monitor. Sometimes jobs may terminate due to error, or lack of resources, which is beyond the control of the ProKnow Webmaster. You may want to resubmit such jobs. All jobs are stored only for a week after their submission.