Construction and Analysis of Amino Acid Substitution Matrices for Optimal Alignment of Microbial Rhodopsin Sequences

2019 ◽  
Vol 74 (1) ◽  
pp. 21-25
Author(s):  
V. N. Novoseletsky ◽  
G. A. Armeev ◽  
K. V. Shaitan
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Optimal Alignment ◽  
Substitution Matrices ◽  
Microbial Rhodopsin ◽  
Amino Acid Substitution Matrices

scholarly journals AN AMINO ACID SUBSTITUTION MATRIX FOR PROTEIN CONFORMATION IDENTIFICATION

2006 ◽  
Vol 04 (03) ◽  
pp. 769-782 ◽  
Author(s):  
XIN LIU ◽  
WEI-MOU ZHENG
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Substitution Matrix ◽  
Structure Alignment ◽  
Amino Acid Substitution Matrix ◽  
Substitution Matrices ◽  
The Matrix ◽  
Structure Relationship ◽  
Improved Performance ◽  
Amino Acid Substitution Matrices

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

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