Bringing LaJolla Back to Life: 3D Structure Search, Then and Now

Table Of Contents

• Intro to LaJolla
• The basic idea, and how it actually works
• Modernizing LaJolla with Claude
• Then: hundreds of machines. Now: five seconds.
• LaJolla as a scientific project - did it stand the test of time?
• Where next?
• Summary
• References

Intro to LaJolla

My PhD thesis was about understanding biomolecules, and one part of that is finding structural similarities between them (full thesis PDF). That work became LaJolla - a 3D alignment algorithm for RNA and proteins, originally published in Algorithms in 2009.