Martin Steinegger
Martin Steinegger
It has todo how the models were trained. According to Richard Evans. Both models AF2 and AF2-multimer were trained in two steps: (1) the initial weights were trained without any...
Please try the alphafold2 (colabfold.com) notebook, which has support for Alphafold-multimer. We do not maintain `AlphaFold2_complexes` anymore.
We do not maintain this notebook. Please contact the Deepmind team here: http://github.com/deepmind/alphafold
Our `colab_batch` (installable through pip) can run batch jobs and keeps the model compiled. It sorts your input sequences by length and pads the input to optimize the amount of...
It seems that the input path could not be resolved. One way to get the correct path is to navigate to your `input_fasta` folder using the file navigator in Colab...
We currently do not support this but we have it on our todo list.
`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 ```...
This is currently not supported. We are discussing what kind of MSA format would work for this.
@jessica-andreani we now support MSAs for complex modeling using an annotated A3M file. Our a3m starts with a header line marked by a `#`. The header consists of two lists...
**Online searches:** Our Colabfold server has ~760GB RAM and keeps full database and index in memory. **Batch searches:** To perform a batch search you require less memory. But its still...