CLICK-Example

Proteins that are sequentially and structurally similar

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Structure Overlap	RMSD	Fragment Score	Topology Score	# CA atoms of 1ang	# CA atoms of 7rsa	Match Size	#Identical Residues
84.55%	1.24	0.99	1.00	123	124	104	33

CLICK superposition of Human Angiogenin, 1ang (salmon) and RNAseA, 7rsa (green) with an SO of 84.55%, RMSD of 1.24Å, and fragment and topology scores of 0.99 and 1.00 respectively.

Proteins that are structurally similar but topologically different

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Structure Overlap	RMSD	Fragment Score	Topology Score	# CA atoms of 1iwmA	# CA atoms of 1oxeA	Match Size	#Identical Residues
63.28%	2.27	0.62	0.57	177	226	112	9

CLICK superposition with different SCOP class of 1iwm:A (salmon & SCOP entry: b.125.1.2) and 1oxe:A (green & SCOP entry: d.22.1.1) with an SO of 63.28%, RMSD of 2.27Å, and fragment and topology scores of 0.62 and 0.57 respectively.

Proteins with multiple chains

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3D Demo

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Structure Overlap	RMSD	Fragment Score	Topology Score	#CA atoms of 1ubp	#CA atoms of 1e9y	Match Size	#Identical Residues
99.49%	0.82	1.00	1.00	790	806	786	463

An alignment between 2 PDB files (1ubp chains A (red), B (yellow), and C (salmon); and 1e9y chains A (cyan) and B (forest green)) of proteins with multiple chains. Chains A and B of 1ubp superimpose onto chain A of 1e9y, and chain C of 1ubp superimpose onto chain B of 1e9y.

DNA double helical structures

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Structure Overlap	RMSD	Fragment Score	Topology Score	# C3' atoms of 1ysa	# C3' atoms of 2ayg	Match Size	# Identical Residues
75.00%	1.80	1.00	1.00	40	36	27	5

CLICK superposition with DNA double helical structures 1ysa (salmon) and 2ayg (green) using representative C3' atom with an SO of 75.00% and RMSD of 1.80Å.

Multi-domain proteins

The first alignment of 1aiv and 1ovt

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The second alignment of 1aiv and 1ovt

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The third alignment of 1aiv and 1ovt

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Structure Overlap	RMSD	Fragment Score	Topology Score	# CA atoms of 1aiv	# CA atoms of 1ovt	Match Size	#Identical Residues
60.12%	2.00	0.75	0.94	686	682	410	242

The first alignment of 1aiv and 1ovt.

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Structure Overlap	RMSD	Fragment Score	Topology Score	# CA atoms of 1aiv	# CA atoms of 1ovt	Match Size	#Identical Residues
11.14%	1.52	0.91	1.00	686	682	76	105

The second alignment of 1aiv and 1ovt.

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Structure Overlap	RMSD	Fragment Score	Topology Score	# CA atoms of 1aiv	# CA atoms of 1ovt	Match Size	#Identical Residues
6.74%	2.21	0.46	1.00	686	682	46	24

10 20 30 40
1aiv 492A:SPPN-SR-LCQLCQGSGG-IPPEKCVASS-HEK-YF-GYTG-A-L-RC:530A
1ovt 492A:SPPNSR-L-CQLCQGS-GGIPPEKCVA-SSHEKYF-G--Y-T-G-A-L:528A

Individual domains in 1aiv (salmon) have a structural equivalence in 1ovt (green), but the relative orientations between these domains differ in the two structures.

Database Search

Protein database search example (24,563 PDB chains)

Human protein database search example (3468 PDB chains)

DNA-Protein complex database search example (2262 structures)

RNA database search example (493 structures)

More information about database searches

Database	Query Structure selected for example search
Protein (24,364 PDB chains)	A 300 residue protein structure (PDB code: 1A3H)
Human protein (3468 PDB chains)	A 100 residue protein structure (PDB code: 5CFH)
DNA Protein complex (2262 PDB structures)	A 86 residue DNA protein complex (PDB code: 1AN2)
RNA (493 PDB structures)	A 32 residue RNA structure (PDB code: 5KVJ)

Runt time: The database search was done when the system was idle (no other resource intensive operation was running on the system). The run time may vary for a new database search depending on the system load and rank of your job in the queue. For an approximate estimate of the run time, please see below link,

Approximate run time estimate: CLICK database search run time estimate

Job Status: User can see the status of their job (whether running or in the queue) by opening the URL (URL is generated after the user submits a job) in their web browser. The page pointed by the URL will report the current status of the job. If the job is completed then the results will be displayed on the same page.