Pairwise Rigid Structure Alignment Program

The program receives as input a pair of PDB files (or uploaded files in PDB format) and finds "large enough" geometrically similar substructures in both molecules, which can be rigidly superimposed.  It returns a set of hypotheses sorted by the size of the superimposed substructures.  The method superimposes the C-alpha atoms of the proteins and is sequence-order independent.


Program url:

Examples: Bacterial electron transferring proteins

1. (Almost identical structures) 1pmy with 1pza

Sequence Alignment:

Score = 116 bits (274), Expect = 8e-26 Identities = 54/120 (45%), Positives = 75/120 (62%)


2. (more distant in sequence) 1pmy with 1aaj

Sequence Alignment:

Score = 32.1 bits (71), Expect = 2e-06 Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 3/78 (3%)

Structural matching:

Result 1: Match size: 78 RMS: 1.44

Rotation: 1.178 -0.059 -2.615 Translation: 30.230 14.864 17.912

Rotations are given in radians for X-Y-Z axes. Rotating space around the X-axis, then around the Y-axis and finally

around the Z-axis would give the required rotation. X-Y-Z translation coordinates are given in Angstrom units.

Note the similar and the different parts of the two proteins.

Note insertions/deletions in loops.

3. (same fold, distant structures) 1svy with 2vik

Both are gelsolin (actin depolymerizing) proteins from slime mold and chicken, respectively.

Sequence Alignment:

(Note, that without the structural information, sequence based alignment can be different than structural alignment!)
Score = 18.8 bits (37), Expect = 0.025
Identities = 23/67 (34%), Positives = 30/67 (44%), Gaps = 12/67 (17%)

          VP+ T S    + GDC+ LL   LT       I+ + G  SS  E   AA     +D E
Query: 88 LGSVAVQ 94
          LG   V+
Sbjct: 69 LGLPLVE 75

Structural Alignment:

To watch only the structurally aligned part, look at 2vik:18-111, 1svy:250-161 (green color).

Note - conservation of the gelsolin fold, insertions and deletions in loops.