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/ ModLink+: structure prediction using protein interactions.
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E-mail Address
Insert a valid e-mail address
* Not mandatory
Upon completion, the server will send an
e-mail
to the provided address with a link to the results page. Alternatively, copy the
session id
and insert it in the
results
page.
Query Sequence
Enter the query sequence in FASTA format
Query sequence must be pasted in the text area in
FASTA format
. Alternatively, use the browse button to upload a file from your local disk containing the query sequence. Please, provide only
one
query sequence (the remaining sequence(s) will be discarded).
more...
Clear
Or, upload file
Advanced options
Proteins Interacting with the Query
Enter sequences in FASTA format of proteins interacting with the query
Proteins interacting with the query (if any are known) can be pasted in the text area in
FASTA format
. Alternatively, use the browse button to upload a file from your local disk containing the protein sequences.
more...
Clear
Or, upload file
Algorithm Parameters
Nº of iterations
8
7
6
5
4
3
2
1
Choose the maximum number iterations
Select the
maximum
number of iterations to be used in
HHblits
from the HH-suite to build a profile of the query sequence. The resulted profile is either a PSI file (for PSI-BLAST restart), A3M file (for HHsearch) or HMM (for PRC). By default, HHblits uses
2 iterations
to construct A3M alignments (
hint
: the more iterations the more time it will take for the script to build the alignment).
more...
Combine with
HHsearch
PRC
PSI-BLAST
Choose the preferred method
Select the preferred method to search for homologs of the query protein in the PDB database.
PSI-BLAST
is based on pairwise sequence alignments while
HHSearch
and
PRC
are based on comparisons of profile hidden Markov models (
hint
PSI-BLAST is faster but HHsearch and PRC are more accurate).
more...
