Improving alphafold performance and applications of alphafold

Stanford University
On Hold
Start as soon as possible
Estimated Engagement Length
6 Months
Completion Date Goal

The project involves the improvements of the alphafold program. The projects includes two parts, improvements of the program and possible applications of it in collaboration with different researchers. The effort will be in coordination of research groups interested in the application of alphafold. 

Specifically the performance improvements involves a hierarchical/diverse aspects of the code, (1)I/O, (2) databases query, (3) multithread/multi process in python, as well as GPU acceleration, and more.   

HPC Resources Needed (if known)
Project Deliverables
1. Understand the performance characteristics and bottlenecks of alphafold2, in terms of CPU, GPU utilization, memory access and utilization, I/O characteristics, as well as database access.
2. Develop a community of researchers collaborating on the application, improvement and development of alphafold and other protein folding software.(optional)
3. optimization of performances of alphafold (optional and dependent on availability of resources)
4. Parallelization of alphafold (optional and dependent on availability of resources and expertise)