Ideal amino acid exchange forms for approximating substitution matrices
Related Experiment Video
Updated: Jul 13, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Piotr Pokarowski1, Andrzej Kloczkowski, Szymon Nowakowski
1Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, Warsaw University, 02-097 Warsaw, Poland. pokar@mimuw.edu.pl
Abstract:
We have analyzed 29 published substitution matrices (SMs) and five statistical protein contact potentials (CPs) for comparison. We find that popular, 'classical' SMs obtained mainly from sequence alignments of globular proteins are mostly correlated by at least a value of 0.9. The BLOSUM62 is the central element of this group. A second group includes SMs derived from alignments of remote homologs or transmembrane proteins. These matrices correlate better with classical SMs (0.8) than among themselves (0.7). A third group consists of intermediate links between SMs and CPs - matrices and potentials that exhibit mutual correlations of at least 0.8. Next, we show that SMs can be approximated with a correlation of 0.9 by expressions c(0) + x(i)x(j) + y(i)y(j) + z(i)z(j), 1
More Related Videos
Related Concept Videos
Ion Exchange
¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons
Ion-Exchange Chromatography
Acid Halides to Amides: Aminolysis
In the first step of the aminolysis mechanism, the amine attacks the carbonyl carbon of the acyl chloride to form a tetrahedral intermediate. In the second step, the carbonyl group is re-formed with the elimination of a chloride...
Protein Complexes with Interchangeable Parts
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Amino acids

