The 3D-Blast algorithm
In order to use 3D-Blast server, it is necessary to provide two protein structures, and to specify a few parameters that control the calculation.

3D-Blast calls the two proteins to be superposed the fixed and mobile structure, respectively. These can be uploaded from PDB files on your PC. For most practical purposes, the fixed and the mobile structures are interchangeable. The 3D-Blast Server removes all water molecules and other "hetero" atoms from the input files.

During the superposition calculation, 3D-Blast keeps the fixed protein fixed and performs a six-degree search in space moving only the moving protein. A score is calculated for each orientation, and the highest-score orientation is assumed to correspond to the best overall 3D shape superposition. This superposition is then used to find possible correspondences between pairs of backbone CA atoms. The distances between these pairs are then input to a Needleman-Wunsch dynamic programming algorithm which is used to find the best global alignment between the two structures. This alignment is used to perform a final least-squares fit of the two structures.

Calculation Device
The "Calculation Device" entry box is used to request that the calculation will be performed by a graphics processor unit (GPU) or the central processor (CPU). Normally the GPU is much faster that the CPU. Multiple GPUs or CPUs will be used if they are available.

Search Order
The Search Order entry box is used to specify the SPF polynomial expansion order of the superposition correlation calculations. The default value of N=10 normally provides good superpositions in almost all cases. Slightly better search results are obtained using N=25 but this is much more computationally-expensive than N=10.

3D-Blast version July 2011