Structural superposition

Question 1

STRUCTURAL SUPERPOSITION
Comparison of Structures:

Answer 1

Determine equivalent points between structures.
Involves suitable representation, optimization function, comparison algorithm, and
evaluation rules.

Question 2

STRUCTURAL SUPERPOSITION
sup vs alignment

Answer 2

Superposition: Pre-defined aligned atoms using translation and rotation; used for
different conformations of the same structure.
Structural Alignment: No prior knowledge of equivalent positions; used for
comparing different or related proteins; involves database searches and identifying
structural relationships.

Question 3

STRUCT SUPERPOS / Representation:

Answer 3

Simplifying the problem by considering one atom per residue (e.g., Cα).

Question 4

SUPERPOSITION TECHNIQUES
Root-Mean-Square Deviation (RMSD):

Answer 4

Measures the average distance between atoms of superimposed proteins.

Question 5

Kabsch Algorithm:

Answer 5

Centers the coordinates, computes cross-covariance matrix, and determines optimal
rotation using Singular Value Decomposition (SVD).

Question 6

Distance Matrix:

Answer 6

L × L matrix representing distances between all pairs of atoms or a representative
atom (e.g., Cα) for each amino acid

Question 7

Contact Map:

Answer 7

Binary matrix indicating contacts (1 for contact, 0 for no contact) using a distance
cutoff (e.g., 8 Å).
Interpretation: Helices, parallel and anti-parallel beta sheets based on contact
patterns relative to the diagonal.

Question 8

SSAP (Sequential Structure Alignment Program):

Answer 8

Compares residue vectors and uses dynamic programming for alignment.
Independent of coordinate reference frames and invariant under rotation.

Question 9

DALI (Distance Matrix Alignment):

Answer 9

Compares distance matrices to find structural similarities.
Fast algorithm: Compares secondary structure elements (SSEs) within a defined
distance.
Accurate algorithm: Recursively aligns matrices to maximize pair scores.

Question 10

Combinatorial Extension (CE):

Answer 10

Finds the longest continuous path of aligned fragment pairs (AFPs).
Uses heuristic path extension and evaluates final alignment with RMSD and Z-score.

Question 11

TM-align (Template Modelling align):

Answer 11

Uses dynamic programming and TM-score to align secondary structures.
Heuristic iterations to stabilize the alignment.

Question 12

TM-score:

Answer 12

Weighs residue pairs at smaller distances more heavily.
Used to evaluate the similarity of protein structures irrespective of size.

Question 13

Heuristic Iterations

Answer 13

Involves rotating structures and applying dynamic programming iteratively to achieve
stable alignments.