- NCBI's BLAST+ suite
- uniref90 seq database prepared for BLAST+
- dssp. This is included in bin/ but you may need to download and compile the source
> cd src/
> make clean
> make
> make install
Run checkchains, to check that the chain in your pdb file is present
cp example/1IAR.pdb ./
> ./bin/checkchains_metsite.pl ./example/1IAR.pdb A
Extract fasta seq
> ./bin/fasta_pdbv3.pl ./example/1IAR.pdb ./1IAR.fasta A
run psiblast
> ncbi-blast-2.2.31+/bin/psiblast -query 1IAR.fasta -inclusion_ethresh 0.001 -num_iterations 3 -num_alignments 0 -out_pssm 1IAR.chk -db uniref90.fasta > 1IAR.bls
run chkparse
> ./bin/chkparse 1IAR.chk > 1IAR.mtx
run mtx_pro
> ./bin/mtx_pro 1IAR.mtx 1IAR.pro
Run dssp
> ./bin/dssp 1IAR.pdb 1IAR.dssp > 1IAR.dsspout
Run seed site find. You must use the chain A you tested for in step 1. You need to provide an ion from this list (note the leading underscore) CU|CA|FE|ZN|MG|MN
> ./bin/seedSiteFind 1IAR.pdb _CU 10 1IAR.pro 1IAR.dssp A
run returnNetCut, keeping the atom choice the same, the second arg is a flag which returns the value for the following FPR:
- 0 = 1%
- 1 = 5%
- 2 = 10%
- 3 = 20%
java -cp 'src/org/ucl/conf/:src' returnNetCut CU 1
Take the float returned and use it as part of the input for met_pred run Met Pred, (i,e: 0.182). Lower case metals this time! And provide a path for the data files and chain id
> ./bin/MetPred 1IAR.pdb.DATA cu 0.182 1IAR_MetPred.pdb A ./data/
As an alternatIve to steps 8 and 9 you can run the python script metpred.py which wraps these two steps together. Basically you pass it the options the previous 2 commands need. Note that the classpath must have full canonical paths, and you must provide a location for the metpred binaries
python ./bin/metpred.py /Users/dbuchan/Code/metsite/src/org/ucl/conf/:/Users/dbuchan/Code/metsite/src/ CU 1 1IAR.pdb.DATA 1IAR_MetPred.pdb A ./bin/ ./data/
or the shell script MetPred_wrapper.sh
/opt/Code/metsite/bin/MetPred_wrapper.sh /opt/Code/metsite CU 1 1IAR.pdb.DATA 1IAR.pdb A