NAGbinder

NAGbinder provides the gold standard dataset of NAG ligand interacting protein chains generated from PDB. Standard techniques were used for generating the dataset, which contains 231 non-redundatnt (40%, CD-HIT) NAG binding protein chains. Dataset is divided into two parts; i) Trainign dataset consists of 186 non-redundant protein chains (1335 NAG interacting residues and 47198 non-interacting residues), ii) Independent/Validation dataset comprises of 45 non-redundant PDB chains (650 NAG interacting residues and 27733 non-interacting residues).

In order to facilitate users in using our dataset effectively, we not only provide NAG binding chains but also binary/pssm patterns. User can download three types of datasets; i)NAG interacting protein chains with annotation, ii) NAG interating and non-interacting protein chain patterns of length 9 amino acids, and iii) PSSM profile for NAG interating and non-interacting protein chains.

Dataset Type1: Protein chains along with the interaction information.

Dataset_Type1	Description	Files
Main	Dataset contains 186 NAG interacting protein chains. Interacting residues have been shown in the form of '+' sign whereas non-interacting is denoted by '-' sign.
Validation	Dataset contains 45 NAG interacting protein chains. Interacting residues have been shown in the form of '+' sign whereas non-interacting is denoted by '-' sign.

Dataset Type2: This dataset type consists of patterns generated from PDB chains.

Dataset_Type2	Description	Files
Main	Dataset contains patterns of window length 9 generated from 186 NAG interacting protein chains. Individual positive and negative patterns are present of each PDB chain.
Validation	Dataset contains patterns of window length 9 generated from 45 NAG interacting protein chains. Individual positive and negative patterns are present of each PDB chain.

Dataset Type2: This dataset type consists of PSSM profile of each patterns generated from PDB chains.

Dataset_Type3	Description	Files
Main	Dataset contains PSSM profiles of each patterns of window length 9 generated from 186 NAG interacting protein chains. Individual positive and negative profiles are present of each PDB chain.
Validation	Dataset contains PSSM profiles of each patterns of window length 9 generated from 45 NAG interacting protein chains. Individual positive and negative profiles are present of each PDB chain.