We’re excited to add a new tool to COSMIC² – AlphaFold2! AlphaFold2 is a highly accurate protein structure prediction algorithm from the DeepMind team. The basics of AlphaFold2 rely on multiple sequence alignments, protein structure databases, and neural network architecting.
While AlphaFold2 is very powerful, it cannot be run on a laptop because of large databases (2.2 TB) and the requirement for CPU/GPUs during prediction. After the release of the code, community-led efforts to put AlphaFold2 on Google’s Colab python-based notebooks for running GPU jobs helped many scientists predict structures of interest. For example, wrapping a number of commands and software together, ColabFold helps users without expertise in bioinformatics to utilize protein structure prediction algorithms.
Even though ColabFold enabled many scientists to run AlphaFold2 on their protein of interest, we wanted to offer the community access to the full AlphaFold2 software package and databases. Since we already run jobs at the San Diego Supercomputer Center Expanse supercomputer, we are happy to host and run this software for everyone.
Learn more on how to run AlphaFold2 on COSMIC2 here!