Figure 3From: Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detectionComparison of heavy-atom contacts query with and without spatial indexing for 11 metafold representatives over 1 ns. With no spatial indexing (circles) applied the calculation of heavy-atom contacts over 1 ns (1000 frames) takes an average of ~20 minutes (n = 6) for the largest protein 1ehe. For the smallest protein, 2adr, the average time taken is around 10 seconds. When spatial indexing is applied (triangles) the is a dramatic decrease in execution time for 1ehe from ~20 minutes to an average of 1 minute 46 seconds. There is almost no change in execution time for 2adr since it is an extremely small protein, such that spatial indexing has little effect.Back to article page