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Frequently asked questions (FAQ)
- When I run PROSPECT with the terminal command "prospect",
the machine told me "prospect: Command not found". What is the problem?
Because prospect has been built for several different operating
systems, each seperate binary must be denoted by it's system type. The
system name has been defined as PVM_ARCH, which is a standard enviromental
varible used by the parallel system PVM. So make sure the $PROSPECT_PATH/bin
is in your PATH, and add the suffix of the system type for the computer you
are on.
- PROSPECT complains that I do not have enough
memory to run a threading. Can I still get some results?
There are several solutions. An expensive solution is to get
a new machine or add more memory. If you have some idea about the sequence
domains, you can cut the protein into several domains and thread the
subsequences one by one. If you do not have any idea about the domain
partition of the query sequence, you can use overlapping subsequences,
such as 1-500, 400-900, 800-1300, 1200-1700, etc. You can also run the
threading without pairwise interactions, which saves the memory and computing
time substantially but may compromise the threading accuracy:
- Is there a size limit for the query protein?
In principle there is none. However, threading with a very
long sequence may not be practical in terms of computing time. We recommend
you to use a sequence with less than 1000 amino acids when you do not use
pairwise interactions, with less than 500 amino acids when you use pairwise
interactions. For larger proteins, you can split them into subsequences (see
the above question).
- The protein seems to have two domains. Should I
split it into two sequences and thread them separately or thread the
whole sequence at the same time? Which way is better?
If you know the protein has two domains, it is better to split
it into two sequences and thread them separately. This will not only
save computing time, but also have better chance to find the correct fold/alignment,
since the search space is much smaller. In particular, sometimes only
one domain has the native-like fold in the database. However, in case
you are not sure about the partition of the two domains, it is better to
run threading on both the whole sequence and the two subsequences. By comparing
the two sets of the results, you may find some clues about the domain
partition and the structure.
- If more than one template turn out to have good
scores, should I only use the one with the best score for MODELLER.
In homology modeling, I was told that more than one good templates are
better and MODELLER will weight them according to the sequence similarity.
What would you suggest in the case of multiple templates from threading?
The current interface between PROSPECT and MODELLER does not
support homology modeling with multiple templates. You may use the alignments
generated by PROSPECT to help the modeling with multiple templates.
However, the focus of PROSPECT is the initial structure model. Hence,
we recommend you to pick up one template to build the model. If you
like to refine the model, please check the instructions in homology modeling
tools.
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