Supplementary Information
Structure Based Barcoding of Proteins
Rahul Metri2, Gaurav Jerath1, Govind Kailas2, Nitin Gacche1, Adityabarna Pal1 &Vibin
Ramakrishnan1, 2
1
Department of Biotechnology, Indian Institute of Technology, Guwahati – 781039. India.
2
Institute of Bioinformatics & Applied Biotechnology, Bangalore – 560100, India
Barcode Identity Index:
Barcode Identity Index (BII): BII is calculated from a metadata of image consisting of numbers
that correspond to the ‘barcode’ and aligning them. In a typical case, Helix is represented as 0,
strand as 1 and the orientation between secondary structures as 3, 4, 5 and 6 based on space
width between 2 bars in the barcode representation. For e.g. 1A41.pdb (Fig. S1) may be
represented as 03030413140304030303030. The number that represents a barcode (query) is
aligned with another number (subject) using Needleman Wunsch algorithm.
eg:
1A41.pdb - 1A4O.pdb
This alignment is scored as follows:
Secondary structure element and its orientation aligned: 2
Secondary structure element aligned its orientation not aligned: 1
Only orientation aligned: 0
All this is added to get align_score
Alignment score and coverage is calculated as:
Q - Query
S - Subject
% Identity Score: Score = (align_score / ((lenQ+(lenQ-1)+lenS+(lenS-1))/2))*100;
% Coverage: Cov=(min(length(S),length(Q))/max(length(S),length(Q)))*100;
1A41
1A40
Fig S1: 3D images of 1A41.pdb and 1A40.pdb.
Table 1: The following table contains the information listing different ligands bound to the
Dihydrofolate reductase molecule (data obtained from PDB).
PDB
Ligand 1
IDs
1DHF
FOLIC ACID
Ligand 2
Ligand 3
Ligand 4
2DHF
5-DEAZAFOLIC
ACID
1OHJ
N-(4-CARBOXY-4-
NADPH DIHYDRO-
{4-[(2,4-DIAMINO-
NICOTINAMIDE-
PTERIDIN- 6-
ADENINE-
YLMETHYL)-
DINUCLEOTIDE
AMINO]-
PHOSPHATE
BENZOYLAMINO}BUTYL)PHTHALAMIC ACID
1HFP
N-[4-[(2,4-
NADP
DIAMINOFURO[2,3D NICOTINAMIDE]PYRIMIDIN-5-
ADENINE-
YL)METHYL]METH
DINUCLEOTIDE
YLAMINO]-
PHOSPHATE
BENZOYL]-LGLUTAMATE
1HFQ
N-[4-[(2,4-
NADP
DIAMINOFURO[2,3D NICOTINAMIDE]PYRIMIDIN-5-
ADENINE-
YL)METHYL]METH
DINUCLEOTIDE
YLAMINO]-
PHOSPHATE
BENZOYL]-L-
GLUTAMATE
1DLS
METHOTREXATE
NADPH DIHYDRONICOTINAMIDEADENINEDINUCLEOTIDE
PHOSPHATE
1U72
METHOTREXATE
NADPH DIHYDRONICOTINAMIDEADENINEDINUCLEOTIDE
PHOSPHATE
1PD9
2,4-DIAMINO-5METHYL-6-[(3,4,5TRIMETHOXY- NMETHYLANILINO)
METHYL]PYRIDO[2,
3-D]PYRIMIDINE
1PDB
SULFATE ION
1KMV
DIMETHYL
(Z)-6-(2-[2,5-
NADPH
SULFATE
SULFOXIDE
DIMETHOXYPHENY
DIHYDRO-
ION
L]ETHEN-1-YL)- 2,4-
NICOTINA
DIAMINO-5-
MIDE-
METHYLPYRIDO[2,3- ADENINED]PYRIMIDINE
DINUCLEO
TIDE
PHOSPHAT
E
1S3V
SULFATE ION
(2R,6S)-6{[methyl(3,4,5trimethoxyphenyl)amin
o]methyl}- 1,2,5,6,7,8hexahydroquinazoline2,4-diamine
1S3W
1S3U
NADP
6-(OCTAHYDRO-1H-
NICOTINAMIDE-
INDOL-1-
ADENINE-
YLMETHYL)DECAH
DINUCLEOTIDE
YDROQUINAZOLINE
PHOSPHATE
- 2,4-DIAMINE
SULFATE ION
(2R,6S)-6{[methyl(3,4,5trimethoxyphenyl)amin
o]methyl}- 1,2,5,6,7,8hexahydroquinazoline2,4-diamine
1PD8
2,4-DIAMINO-5-
NADPH DIHYDRO-
METHYL-6-[(3,4,5-
NICOTINAMIDE-
TRIMETHOXY- N-
ADENINE-
METHYLANILINO)
DINUCLEOTIDE
METHYL]PYRIDO[2,
PHOSPHATE
3-D]PYRIMIDINE
2C2T
(S)-2,4-DIAMINO-5-
(R)-2,4-DIAMINO-5-
GLYCEROL NADPH
((7,8-
((7,8-
DIHYDRO-
DICARBAUNDECAB
DICARBAUNDECAB
NICOTINAMI
ORAN- 7-
ORAN- 7-
DE-
YL)METHYL)-6-
YL)METHYL)-6-
ADENINE-
METHYLPYRIMIDIN METHYLPYRIMIDIN
DINUCLEOTI
E
DE
E
PHOSPHATE
2C2S
2,4-DIAMINO-5-(1-O- GLYCEROL
NADPH
CARBORANYLMET
DIHYDRO-
HYL)-6-
NICOTINA
METHYLPYRIMIDIN
MIDE-
E
ADENINEDINUCLEO
TIDE
PHOSPHAT
E
1MVS
2,4-DIAMINO-6-[N-
SULFATE ION
(3',4',5'TRIMETHOXYBENZ
YL)- NMETHYLAMINO]PY
RIDO[2,3D]PYRIMIDINE
1BOZ
NADPH DIHYDRO-
N6-(2,5-
NICOTINAMIDE-
DIMETHOXY-
ADENINE-
BENZYL)-N6-
DINUCLEOTIDE
METHYL-
PHOSPHATE
PYRIDO[2,3D]PYRIMIDINE-2,4,6TRIAMINE
Barcode image of 1M65_A
Figure S2: Modified image to exemplify the Possibility of incorporating barcode as an additional
structure representation in huge databases and molecular repositories.