hello, i used to use CPORT for the active and passive site prediction in order to run a protein-protein docking analysis in HADDOCK , but now as it is not available i was trying to use WHISKY.
yet, i am having a lot of doubts concerning the alignment imput i need to add …
I have several MSA.fa, AA.fa and codonMSA.fa alignments with the sequences I used to run a positive selection analysis and then i use those same sequences for predicting protein structures.
But whenever I try to imput the .pdb file, i select the A chain (that is the one in my protein) and any of mine alignments ( MSA.fa, AA.fa or codonMSA.fa), selecting FASTA, they are not working and reporting an error
Could someone help me understanding what could be wrong here ?
Thank you so much in advance,
Best regards and thank you for creating such nice tools
Are you using the web server?
could you maybe give me some extra help here ? I would really appreciate it if I could run the final haddocks for the protein-protein interactions i am studying in order to publish as soon as possible
for example, I am working with the Sirt1 protein in chinchila lanigera
(seq: NLLLSDELVTNGFHSCESDEDDRASHASSSDWTPRPRIGPYTFVQQHLMIGTDPRTILKDLLPETIPPPELD
DMTLWQIVINILSEPPKRKKRKDINTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFP
DLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHQFIALSDKEGKLLRNYTQNIDTLEQVAGIQRII
QCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPPDEPLAIMKPEIVFFGENLPEQFHRAMKYDKDE
VDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLCCNP
VKLSEITEKPPRTQKELVHLSEFPPTPLHISEDSSSPERASPDSSVVATLLEQAAKSSADGVDASESKDYAE
EKPQEVQTSTRRAESVSVESPDLKDTGSNTAEKSGRTSVAETVRKCWPNRLAKEQISKRLDGNQYLFLPPNR
YIFHGAEVYSDSEDDVLSSSSCGSNSDSGTCQSPSLEEPLEDESEIEEFYNGLEDDPEVPEIAGGTGFGADG
GDHEAVNDTISTKQEVTDMNCPSNKS)
I have the predicted 3D structure (both by alphafold and by I-tasser):
c_lanigera_sirt1_alphafold.pdb (734.3 KB)
c_lanigera_sirt1_model1.pdb (733.9 KB)
and I have also the MSA alignment produces by a pipeline of positive selection prediction in fasta file (both at coden and AA level), where among other species chinchila is included, but its not the first to appear, as I used Mus musculus as the reference sequence
ENSMUSG00000020063_codonMSA.txt (43.8 KB)
(could only attach in .txt format, but i have it in .fa)
this doesnt seem to work in WHISKY, so I try to search for a possible homologue with HSSP in protein databank, but i can´t find the HSSP ID anywhere…and even went to the link you propose and try to download the HSSP database myself, but their server is down… and its impossible for me to retrieve data
could you please suggest another way ?
I just want the active and passive residues in oder to make protein-protein haddock predictions…
I’ve also tried usinf HADDOCK 2.4 without the active and passive residues, but the haddock score of the result is really not good
Thanks for all the help and great work so far in advance 