CLICK Server

Topology Independent Comparison of Biomolecular 3D Structures

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The example of database search is available at http://mspc.bii.a-star.edu.sg/minhn/DNA_protein.html

Proteins that are sequentially, and structurally similar

Picture rendered using Chimera (http://www.cgl.ucsf.edu/chimera/)

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 with multiple chains

Picture rendered using Chimera (http://www.cgl.ucsf.edu/chimera/)

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.

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Proteins that are structurally similar but topologically different

Picture rendered using Chimera (http://www.cgl.ucsf.edu/chimera/)

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.

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Multi-domain proteins

The first alignment of 1aiv and 1ovt

Picture rendered using Chimera (http://www.cgl.ucsf.edu/chimera/)

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 second alignment of 1aiv and 1ovt

Picture rendered using Chimera (http://www.cgl.ucsf.edu/chimera/)

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 third alignment of 1aiv and 1ovt

Picture rendered using Chimera (http://www.cgl.ucsf.edu/chimera/)

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.

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DNA double helical structures

Picture rendered using Chimera (http://www.cgl.ucsf.edu/chimera/)

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

                    10                          10
1ysa    7A:TGACTCATCCAGT-T:20A     21B:AA-ACTGGATGAGTCA:35B
2ayg    1C:GCAACCGAATTCGGT:15C      5D:C-C-GAATTCGGTTGC:18D

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.

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