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Protocols

AAindex specifications

Information


Unique identifier OMICS_14775
Name AAindex
Alternative name Amino-Acid Index
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 9.0
Maintained Yes

Documentation


Maintainer


  • person_outline Shuichi Kawashima

Publications for Amino-Acid Index

AAindex citations

 (63)
library_books

MFS Transporters and GABA Metabolism Are Involved in the Self Defense Against DON in Fusarium graminearum

2018
Front Plant Sci
PMCID: 5908970
PMID: 29706976
DOI: 10.3389/fpls.2018.00438

[…] performed against the curated transporter classification database (). To remove the false positive predictions, the candidate transporters and their potential substrates were further examined by the AAindex and PSSM-based methods as developed in TrSSP (). […]

library_books

AIPpred: Sequence Based Prediction of Anti inflammatory Peptides Using Random Forest

2018
Front Pharmacol
PMCID: 5881105
PMID: 29636690
DOI: 10.3389/fphar.2018.00276

[…] a feature selection protocol, which has been implemented in addressing various biological problems (; , ). First, we studied the contribution of individual composition [amino acid composition (AAC), amino acid index (AAI), dipeptide composition (DPC), chain-transition-composition (CTD), and physicochemical properties (PCP)] in AIP prediction. Since the DPC-based model significantly outperformed o […]

library_books

Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction

2018
BMC Genomics
PMCID: 5781056
PMID: 29363424
DOI: 10.1186/s12864-017-4336-8

[…] ers []), SucPred which is a learning algorithm that only regards positive and unlabeled samples [], SuccinSite that incorporates encoding schemes such as k-spaced amino acid pairs, binary scoring and amino acid index properties as input to a random forest classifier [], and SuccFind which employs evolutionary information along with an improved feature strategy for optimization [].However, none of […]

library_books

CIPPN: computational identification of protein pupylation sites by using neural network

2017
Oncotarget
PMCID: 5752488
PMID: 29312575
DOI: 10.18632/oncotarget.22335

[…] ne of the important future research topics is to discover the size of hidden layers and hidden nodes with difference type data structures.From the Table , we can find that the performances of feature AAIndex PCA can clear distinct the difference between the negative samples and the positive ones. It was pointed that the first proposed feature extracting method achieves the average Acc value of 83. […]

call_split

Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach

2017
J Proteome Res
PMCID: 5737412
PMID: 28960077
DOI: 10.1021/acs.jproteome.7b00388
call_split See protocol

[…] percentage of different classes of amino acids (tiny, small, aliphatic, aromatic, nonpolar, polar, charged, positive or negative amino acids), and the mean value of the characteristics stored in the AAindex database (release 9.1).We sorted tryptic peptides based on the number of observations in proteomic experiments and compared the properties of the most observed peptides with the less observed […]

library_books

A systematic identification of species specific protein succinylation sites using joint element features information

2017
PMCID: 5584904
PMID: 28894368
DOI: 10.2147/IJN.S140875

[…] composition with SVM classifier. In addition, an SVM-based predictor SuccFind utilizing the amino acid frequency-based composition of k-spaced amino acid pair (CKSAAP) and a single amino acid index (AAindex) properties was developed. We developed a random forest (RF)-based predictor SuccinSite, in which the three informative sequence encoding features, that is, CKSAAP, binary, and the selected AA […]

Citations

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AAindex institution(s)
Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan; Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, Warsaw University, Warsaw, Poland; Faculty of Geodesy and Cartography, Warsaw University of Technology, Warsaw, Poland; Laboratory of Theory of Biopolymers, Faculty of Chemistry, Warsaw University, Warsaw, Poland; Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
AAindex funding source(s)
This work was supported by grants from the Ministry of Education, Culture, Sports, Science and Technology, and the Japan Science and Technology Agency.

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