Martin Steinegger

icon indicating a website link http://steineggerlab.com/ icon indicating an email [email protected]

icon company Seoul National University icon location Korea icon location Scientist and Engineer. Associate Professor at Seoul National University.

Results 234 comments of Martin Steinegger

Run Prediction halted

Our server had an outage. We restarted it. It should work again. Sorry for the inconvenience.

Run Prediction halted

Thank you so much for the kind words @jfbazan. ColabFold is team effort. Actually @milot-mirdita fixed the server. :) Happy holidays to you too.

--msa-mode options without brackets and spaces?

Probably the best idea would be to submit the job through a script. Alternative the following might work (not tested): ``` qsub -q ${QUEUE_NAME} -V -pe smp ${Num_Processes} -l gpu=${Num_GPUs}...

Aberrant 3D modeling of a multiprotein complex leads to the formation of a covalent interprotein bond Arginine - Leucine

AlphaFold2 as well as AlphaFold-multimer were trained to be robust against mutations. Both models are not the right tool to model single point mutation effects.

on running colabfold locally

Unfortunately, we currently do not have a solution how to store the paired+unpaired MSA for complex predictions. The `msa.pickle` might be a solution but we need a script that converts...

on running colabfold locally

@xvazquezc is should not use the MMseqs2 server if you provide a a3m input. Also our a3m server does not do any folding, it only generates the input MSAs. Their...

on running colabfold locally

`colabfold_search` as well as `colabfold_batch` supports batch complex predictions. Just provide a fasta or csv fle with your complex sequences. Following is a `example.fasta`: ``` >1 PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK:PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK >2 PIAQIHILEGRSDEQKE:PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK ```...

pdbfixer

Do you have an input to reproduce the issue?

colabfold_batch still runs a MSA query even if `--msa-mode single_sequence`

I pushed some change that should fix it. Could you give it a try again please?

MMseqs2 search results with Taxonomy ID using uniref30_2103 database and colabfold_envdb_202108 database

ColabfoldDB does not contain taxonomical information since the sequences are from various metagenomic sources, only UniRef30 has taxonomical information. We recently uploaded the UniRef taxonomy information to our ftp [colabfold.mmseqs.com](https://colabfold.mmseqs.com)....