AAindex: Amino Acid Index Database

Release 9.2, Feb 2017

Introduction

An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biological properties of amino acids. The AAindex1 section of the Amino Acid Index Database is a collection of published indices together with the result of cluster analysis using the correlation coefficient as the distance between two indices. This section currently contains 566 indices.

Another important feature of amino acids that can be represented numerically is the similarity between amino acids. Thus, a similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches. The AAindex2 section of the Amino Acid Index Database is a collection of published amino acid mutation matrices together with the result of cluster analysis. This section currently contains 94 matrices.

In the release 9.0, we added a collection of published protein pairwise contact potentials to AAindex as AAindex3. This section currently contains 47 contact potential matrices.

How to search AAindex

AAindex entries can be retrieved by keyword search against the description lines of AAindex (D line in each entry) using DBGET. For example, the user can retrieve a list of entries to input keywors such as 'alpha-helix' or 'hydrophobicity' on the text-box of AAindx home page or the DBGET search page. In the DBGET system, the "bfind" mode is used to get the list of entries including the specified keywords and the "bget" mode is used to get an database entry by specifing an entry ID.

AAindex Home http://www.genome.jp/aaindex/
AAindex search by DBGET http://www.genome.jp/dbget-bin/www_bfind?aaindex

Important Changes

References

Please cite the following references when making use of the database:

Correspondence

Shuichi Kawashima
Database Center for Life Science,
Joint Support-Center for Data Science Research
Research Organization of Information and Systems
Univ. of Tokyo Kashiwa-no-ha Campus Station Satellite 6F.
178-4-4 Wakashiba, Kashiwa-shi, Chiba 277-0871, JAPAN
E-mail: kwsm@dbcls.rois.ac.jp

Data format of AAindex

Data Format of AAindex1
************************************************************************
*                                                                      *
* Each entry has the following format.                                 *
*                                                                      *
* H Accession number                                                   *
* D Data description                                                   *
* R PMID                                                               *
* A Author(s)                                                          *
* T Title of the article                                               *
* J Journal reference                                                  *
* * Comment or missing                                                 *
* C Accession numbers of similar entries with the correlation          *
*   coefficients of 0.8 (-0.8) or more (less).                         *
*   Notice: The correlation coefficient is calculated with zeros       *
*   filled for missing values.                                         *
* I Amino acid index data in the following order                       *
*   Ala    Arg    Asn    Asp    Cys    Gln    Glu    Gly    His    Ile *
*   Leu    Lys    Met    Phe    Pro    Ser    Thr    Trp    Tyr    Val *
* //                                                                   *
************************************************************************
Data Format of AAindex2 and AAindex3
************************************************************************
*                                                                      *
* Each entry has the following format.                                 *
*                                                                      *
* H Accession number                                                   *
* D Data description                                                   *
* R PMID                                                               *
* A Author(s)                                                          *
* T Title of the article                                               *
* J Journal reference                                                  *
* * Comment or missing                                                 *
* M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV           *
*   AA                                                                 *
*   AR RR                                                              *
*   AN RN NN                                                           *
*   AD RD ND DD                                                        *
*   AC RC NC DC CC                                                     *
*   AQ RQ NQ DQ CQ QQ                                                  *
*   AE RE NE DE CE QE EE                                               *
*   AG RG NG DG CG QG EG GG                                            *
*   AH RH NH DH CH QH EH GH HH                                         *
*   AI RI NI DI CI QI EI GI HI II                                      *
*   AL RL NL DL CL QL EL GL HL IL LL                                   *
*   AK RK NK DK CK QK EK GK HK IK LK KK                                *
*   AM RM NM DM CM QM EM GM HM IM LM KM MM                             *
*   AF RF NF DF CF QF EF GF HF IF LF KF MF FF                          *
*   AP RP NP DP CP QP EP GP HP IP LP KP MP FP PP                       *
*   AS RS NS DS CS QS ES GS HS IS LS KS MS FS PS SS                    *
*   AT RT NT DT CT QT ET GT HT IT LT KT MT FT PT ST TT                 *
*   AW RW NW DW CW QW EW GW HW IW LW KW MW FW PW SW TW WW              *
*   AY RY NY DY CY QY EY GY HY IY LY KY MY FY PY SY TY WY YY           *
*   AV RV NV DV CV QV EV GV HV IV LV KV MV FV PV SV TV WV YV VV        *
* //                                                                   *
************************************************************************