ColabFold Alternatives

ColabFold reviews and mentions

• Can I successfully model a small protein from scratch?
  1 project | /r/bioinformatics | 23 Oct 2022
• JMol, Mol*3D, PyMol: Anyway to move two proteins relative to each other?
  1 project | /r/bioinformatics | 21 Aug 2022

  Thanks for the info. Any opinions on ColabFold?

• What is better right now? AlphaFold or RoseTTAFold?
  1 project | /r/bioinformatics | 4 Jun 2022

  I'm on the software & infrastructure side of things, so perhaps don't have the depth of the answer you're looking for, and would be happy to be corrected. But as far as I understand from the scientists on our team is that "it depends". Both can get results that are remarkably close to one another, but both can also disagree, so it's hard to say what's "better" - it depends on what you consider the ground truth for your experiments, and a number of other factors such as the length of the sequences you're working with. Both are able to predict structure from sequence, recover sequence from structure, as well as "hallucinate" structure and sequence, so it can be helpful to use both to validate your results and increase your confidence. I assume you've seen the ColabFold notebooks, so it should be easy to compare them against each other for your use case.

• Is there any software that can predict if two amino acid sequences would interact?
  3 projects | /r/bioinformatics | 6 May 2022

  a word of warning, the requirements are pretty high, if the sequences are not too long try one of the notebooks: https://github.com/sokrypton/ColabFold

• Advice on Alpha Fold 2.0
  1 project | /r/bioinformatics | 25 Jan 2022

  In the ColabFold GitHub README there is a description of differences between ColabFold, DeepMind's version, and others. Apparently, the usage of templates and mmseqs2 was not available in the default DeepMind's implementation and was added in ColabFold. https://github.com/sokrypton/ColabFold

• I managed to get Googles deepmind Alphafold running. I modeled segment of DNA from M.Genitalia and also compared it to the much less accurate method of homology modeling that was used in days past.
  2 projects | /r/Biochemistry | 3 Jan 2022
• Deep-learning algorithms can now predict a protein’s 3D shape from its linear sequence — a huge boon to structural biologists
  2 projects | /r/technology | 26 Nov 2021
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  www.saashub.com | 10 May 2024

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