PMID- 27249328
OWN - NLM
STAT- MEDLINE
DCOM- 20171017
LR  - 20220317
IS  - 1557-8666 (Electronic)
IS  - 1066-5277 (Linking)
VI  - 23
IP  - 8
DP  - 2016 Aug
TI  - A Complex Prime Numerical Representation of Amino Acids for Protein Function 
      Comparison.
PG  - 669-77
LID - 10.1089/cmb.2015.0178 [doi]
AB  - Computationally assessing the functional similarity between proteins is an 
      important task of bioinformatics research. It can help molecular biologists 
      transfer knowledge on certain proteins to others and hence reduce the amount of 
      tedious and costly benchwork. Representation of amino acids, the building blocks 
      of proteins, plays an important role in achieving this goal. Compared with 
      symbolic representation, representing amino acids numerically can expand our 
      ability to analyze proteins, including comparing the functional similarity of 
      them. Among the state-of-the-art methods, electro-ion interaction pseudopotential 
      (EIIP) is widely adopted for the numerical representation of amino acids. 
      However, it could suffer from degeneracy that two different amino acid sequences 
      have the same numerical representation, due to the design of EIIP. In light of 
      this challenge, we propose a complex prime numerical representation (CPNR) of 
      amino acids, inspired by the similarity between a pattern among prime numbers and 
      the number of codons of amino acids. To empirically assess the effectiveness of 
      the proposed method, we compare CPNR against EIIP. Experimental results 
      demonstrate that the proposed method CPNR always achieves better performance than 
      EIIP. We also develop a framework to combine the advantages of CPNR and EIIP, 
      which enables us to improve the performance and study the unique characteristics 
      of different representations.
FAU - Chen, Duo
AU  - Chen D
AD  - 1 School of Biological Science and Medical Engineering, Southeast University , 
      Nanjing, China .
FAU - Wang, Jiasong
AU  - Wang J
AD  - 2 Department of Mathematics, Nanjing University , Nanjing, China .
FAU - Yan, Ming
AU  - Yan M
AD  - 3 Department of Biotechnology & Pharmaceutical Engineering, Nanjing Tech 
      University , Nanjing, China .
FAU - Bao, Forrest Sheng
AU  - Bao FS
AD  - 4 Department of Electrical and Computer Engineering, University of Akron , Akron, 
      Ohio.
LA  - eng
PT  - Journal Article
DEP - 20160601
PL  - United States
TA  - J Comput Biol
JT  - Journal of computational biology : a journal of computational molecular cell 
      biology
JID - 9433358
RN  - 0 (Amino Acids)
RN  - 0 (Proteins)
SB  - IM
MH  - *Algorithms
MH  - Amino Acids/*chemistry
MH  - Computational Biology/*methods
MH  - Databases, Protein
MH  - Humans
MH  - Models, Molecular
MH  - Proteins/*chemistry/*metabolism
MH  - Sequence Analysis, Protein/*methods
OTO - NOTNLM
OT  - CPNR
OT  - EIIP
OT  - numerical representation
OT  - protein
OT  - sequence comparison
EDAT- 2016/06/02 06:00
MHDA- 2017/10/19 06:00
CRDT- 2016/06/02 06:00
PHST- 2016/06/02 06:00 [entrez]
PHST- 2016/06/02 06:00 [pubmed]
PHST- 2017/10/19 06:00 [medline]
AID - 10.1089/cmb.2015.0178 [doi]
PST - ppublish
SO  - J Comput Biol. 2016 Aug;23(8):669-77. doi: 10.1089/cmb.2015.0178. Epub 2016 Jun 
      1.