How to run Boltz-1? An AI-based Molecular Structure Prediction Tool.

[@Abdulrahman-wv6tm]

That was very helpful thank you from Iraq

[@Bioinformaticsinsights]

My pleasure

[@ehedaymaz]

Hello firstly thank you for the great video 🙏🏻 Can you suggest a especially web tool to predict 3D DNA structure? Thank you in advance ☺️🙏🏻

[@Bioinformaticsinsights]

Why are you looking for another tool. Why not try AlphaFold3? kzbin.info/www/bejne/mJeopamqjK94fck

[@RichardXu-i4u]

I am currently working on comparing Boltz-1, Protein X, and the AlphaFold server for predicting the complex. While the AlphaFold server successfully predicts large protein complexes, I encountered error messages when attempting similar predictions with Boltz-1 and Protein X. Could you please clarify whether Boltz-1 and Protein X are capable of predicting large protein complexes? Additionally, I would like to know the maximum amino acid limit for these tools.

[@Bioinformaticsinsights]

@Richard I have noticed the similar results, in my case exceeding ~ 1000 - 1200 aa put the server unresponsive. Though all the three Chai-1, Boltz-1 and AlphaFold3 are at comparable level below 1000 aa. I look into documentation, and if a solid answer, for sure will paste it here. Cheers

[@Scholarshahabuddin]

Sir please suggest me the best way to predict the structure of a protein, either with pymol, alphafold or this one?

[@Bioinformaticsinsights]

First of all, PyMOL can not predict the structure, it is a visualizer, unless you use some plugin. You can predict the structure with AlphaFold3 or Boltz-1...Both of them will give almost similar results and the best ones too.

[@Scholarshahabuddin]

@@Bioinformaticsinsights thank you sir

[@raycwm6688]

Can you input short peptide as ligand?

[@Bioinformaticsinsights]

Yes, you can use short peptides by pasting peptide sequence in the first tab

[@MuhammadHamza-mb7wk]

Sir can we use this as compared to alpha fold 3? If alpha fold 3 is the strongest tool among all the prediction tools, can we say that, we can rely on alpha fold 3? Or do we need to use other tools too for the structure prediction?

[@Bioinformaticsinsights]

As I mentioned in the video, Boltz gives performance and Accuracy similar to AF3. In fact, Boltz is better but stating it a better candidate at this stage, will be too early.

[@MuhammadHamza-mb7wk]

@Bioinformaticsinsights thank you sir ❤️

[@Abdulrahman-wv6tm]

the colab link doesnt work?

[@Bioinformaticsinsights]

Dear, I have rechecked and found it fine. Can you paste the step here, where it sticks?