International Journal of Biomedical Imaging

Research Article

Protein Surface Characterization Using an Invariant Descriptor

Table 2

(a) Top 50 hits using DRC for a query protein structure from the EGF family on DATASET-B. Annotations in bold correspond to members of the EGF family, predicted proteins, or uncharacterized proteins


Protein	Chain	Distance	Protein name annotation	Rank

2a2q	L	0.0000	COAGULATION FACTOR VII	1
2fir	L	1.4925	COAGULATION FACTOR VII LIGHT CHAIN	2
2zp0	L	1.5545	FACTOR VII LIGHT CHAIN	3
1wtg	L	1.5628	COAGULATION FACTOR VII	4
1wun	L	1.5844	COAGULATION FACTOR VII	5
2b8o	L	1.6305	COAGULATION FACTOR VII LIGHT CHAIN	6
2zwl	L	1.6379	FACTOR VII LIGHT CHAIN	7
2zzu	L	1.6536	FACTOR VII LIGHT CHAIN	8
1wqv	L	1.6816	COAGULATION FACTOR VII	9
2ec9	L	1.6832	COAGULATION FACTOR VII	10
1dan	L	1.7655	BLOOD COAGULATION FACTOR VIIA	11
1wss	L	1.7659	COAGULATION FACTOR VII	12
2puq	L	1.7692	COAGULATION FACTOR VII	13
1fak	L	1.7934	PROTEIN (BLOOD COAGULATION FACTOR VIIA)	14
2b7d	L	1.8024	COAGULATION FACTOR VII	15
6acn	A	1.8061	ACONITASE	16
2aer	L	1.8120	COAGULATION FACTOR VII	17
2aei	L	1.8164	COAGULATION FACTOR VII	18
2flr	L	1.8196	COAGULATION FACTOR VII	19
3ela	L	1.8668	COAGULATION FACTOR VII LIGHT CHAIN	20
1z6j	L	1.8859	COAGULATION FACTOR VII	21
2f9b	L	1.9027	COAGULATION FACTOR VII	22
3phs	A	1.9169	CELL WALL SURFACE ANCHOR FAMILY PROTEIN	23
3n54	B	1.9263	SPORE GERMINATION PROTEIN B3	24
3qbp	B	1.9264	FUMARASE FUM	25
3ma9	L	1.9367	TRANSMEMBRANE GLYCOPROTEIN	26
3mt0	A	1.9921	UNCHARACTERIZED PROTEIN PA1789	27
3lgu	A	2.0004	PROTEASE DEGS	28
3m7i	A	2.0071	TRANSKETOLASE	29
1qfk	L	2.0096	PROTEIN (COAGULATION FACTOR VIIA (LIGHT CHAIN))	30
3n9t	A	2.0169	PNPC	31
3pxz	A	2.0235	CELL DIVISION PROTEIN KINASE 2	32
2flb	L	2.0257	COAGULATION FACTOR VII	33
3lh1	A	2.0289	PROTEASE DEGS	34
3nlc	A	2.0300	UNCHARACTERIZED PROTEIN VP0956	35
3no5	C	2.0302	UNCHARACTERIZED PROTEIN	36
3msq	C	2.0347	PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN	37
3ryk	A	2.0389	DTDP-4-DEHYDRORHSMNOSE 3,5-EPIMERASE	38
3m4a	A	2.0444	PUTATIVE TYPE I TOPOISOMERASE	39
3n3n	B	2.0444	CATALASE-PEROXIDASE	40
2R3G	A	2.0456	CELL DIVISION PROTEIN KINASE 2	41
2R3I	A	2.0465	CELL DIVISION PROTEIN KINASE 2	42
3o0r	L	2.0473	ANTIBODY FAB FRAGMENT LIGHT CHAIN	43
3n3p	B	2.0490	CATALASE-PEROXIDASE	44
3nfh	A	2.0492	DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49	45
3qfk	A	2.0501	UNCHARACTERIZED PROTEIN	46
3n5h	F	2.0517	FARNESYL PYROPHOSPHATE SYNTHASE	47
3n3o	B	2.0529	CATALASE-PEROXIDASE	48
3o78	B	2.0548	CHIMERA PROTEIN OF PEPTIDE OF MYOSIN LIGHT CHAIN SMOOTH MUSCLE, GREEN FLUORESCENT PROTEIN, GREEN FLUORESCENT CALMODULIN	49
3luy	A	2.0570	PROBABLE CHORISMATE MUTASE	50

(b) Top 50 hits using DRC for a query protein structure from the COX-2 family on DATASET-B. Annotations in bold correspond to members of the COX-2 family, predicted proteins, or uncharacterized proteins


Protein	Chain	Distance	Protein name annotation	Rank

2zxw	B	0.0000	CYTOCHROME C OXIDASE SUBUNIT 2	1
2eil	B	1.3914	CYTOCHROME C OXIDASE SUBUNIT 2	2
2eij	B	1.5853	CYTOCHROME C OXIDASE SUBUNIT 2	3
3ag4	B	1.6147	CYTOCHROME C OXIDASE SUBUNIT 2	4
2dys	B	1.6991	CYTOCHROME C OXIDASE SUBUNIT 2	5
3ag1	B	1.8159	CYTOCHROME C OXIDASE SUBUNIT 2	6
2eim	B	1.8824	CYTOCHROME C OXIDASE SUBUNIT 2	7
3ag2	B	2.0173	CYTOCHROME C OXIDASE SUBUNIT 2	8
2occ	B	2.0631	CYTOCHROME C OXIDASE	9
3abl	B	2.1404	CYTOCHROME C OXIDASE SUBUNIT 2	10
2eik	B	2.1413	CYTOCHROME C OXIDASE SUBUNIT 2	11
3abm	B	2.1454	CYTOCHROME C OXIDASE SUBUNIT 2	12
1v55	B	2.1489	CYTOCHROME C OXIDASE POLYPEPTIDE II	13
2dyr	B	2.2044	CYTOCHROME C OXIDASE SUBUNIT 2	14
2ein	B	2.2628	CYTOCHROME C OXIDASE SUBUNIT 2	15
1v54	B	2.2976	CYTOCHROME C OXIDASE POLYPEPTIDE II	16
3n56	B	2.4226	INSULIN-DEGRADING ENZYME	17
3abk	B	2.4502	CYTOCHROME C OXIDASE SUBUNIT 2	18
3p42	A	2.4785	PREDICTED PROTEIN	19
3r2u	B	2.4846	METALLO-BETA-LACTAMASE FAMILY PROTEIN	20
3msu	B	2.4920	CITRATE SYNTHASE	21
3ag3	B	2.4950	CYTOCHROME C OXIDASE SUBUNIT 2	22
3ntd	B	2.5052	FAD-DEPENDENT PYRIDINE NUCLEOTIDE-DISULPHIDE OXIDOREDUCTASE	23
3ngi	A	2.5055	DNA POLYMERASE	24
7xim	B	2.5198	D-XYLOSE ISOMERASE	25
3mjy	A	2.5206	DIHYDROOROTATE DEHYDROGENASE	26
3nva	B	2.5391	CTP SYNTHASE	27
3lm3	A	2.5433	UNCHARACTERIZED PROTEIN	28
3ppn	B	2.5511	GLYCINE BETAINE/CARNITINE/CHOLINE-BINDING PROTEIN	29
3o98	B	2.5557	BIFUNCTIONAL GLUTATHIONYLSPERMIDINE SYNTHETASE/AM	30
3pom	B	2.5558	RETINOBLASTOMA-ASSOCIATED PROTEIN	31
3nt6	B	2.5656	FAD-DEPENDENT PYRIDINE NUCLEOTIDE-DISULPHIDE OXIDOREDUCTASE	32
5lym	B	2.5690	LYSOZYME	33
3n1y	B	2.5728	TOLUENE O-XYLENE MONOOXYGENASE COMPONENT	34
1occ	B	2.5772	CYTOCHROME C OXIDASE	35
3lxt	D	2.5860	GLUTATHIONE S TRANSFERASE	36
2q70	B	2.5922	ESTROGEN RECEPTOR	37
3l49	B	2.5930	ABC SUGAR (RIBOSE) TRANSPORTER, PERIPLASMIC SUBSTRATE-BINDING SUBUNIT	38
3pvq	A	2.5944	DIPEPTIDYL-PEPTIDASE VI	39
3puf	B	2.6032	RIBONUCLEASE H2 SUBUNIT B	40
3mve	B	2.6077	UPF0255 PROTEIN VV1_0328	41
3ld2	B	2.6143	PUTATIVE ACETYLTRANSFERASE	42
3ne6	A	2.6160	DNA POLYMERASE	43
3qae	A	2.6179	3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE	44
3qh8	A	2.6197	BETA-LACTAMASE-LIKE	45
3m3r	A	2.6215	ALPHA-HEMOLYSIN	46
3nrb	B	2.6234	FORMYLTETRAHYDROFOLATE DEFORMYLASE	47
3n05	B	2.6240	NH(3)-DEPENDENT NAD(+) SYNTHETASE	48
3m2l	A	2.6324	ALPHA-HEMOLYSIN	49
3pns	B	2.6357	URIDINE PHOSPHORYLASE	50