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ChemMine Demo

This demonstration of ChemMine's utilities uses the bioactive compounds that were discovered in the following chemical genomics study:



Surpin M, Rojas-Pierce M, Carter C, Hicks G, Vasquez J, Raikhel N (2005) The Power of Chemical Genomics to Study the Link between Endomembrane System Components and the Gravitropic Response. Proc Nat Acad Sci USA, 102: 4902-4907.

Retrieve Compounds by IDs and Explore Annotation Pages

Paste the following compound identifiers into the query field of the Annotation Search page. Select 'ChemBridge Microformat' as database, choose the option 'Compond ID' as query field and click the 'Search' button. The returned table lists some basic property information about the compounds. The table can be sorted by clicking on the arrows next to the column titles. The compound images and the physicochemical property descriptors of all compounds can be displayed in a similar table format by selecting on the Annotation Search page the options 'Extended View' or 'Show JOELib descriptors', respectively.

Compound identifiers from Surpin et al, 2005: 

	5135414 5271050	5320396 5363833
	5403629	5549214	5694085	5850247
	5900360	5929549	5940365	6054314
	6067962	6097727	6099904	6100411
	6110182	6123583	6124497	6126152
	6138949	6139453	6139547	6141988
	6145308	6149377	6155336	6157413
	6160287	6162761	6163281	6164506
	6220480	6241121













Demo Substructure Search

Open the Structure Similarity Search page, paste the following structure string into the SMILES field and search the 'ChemBridge Microformat' database with the 'Substructure Search' option.













Demo Similarity Search

Open the Structure Similarity Search' page, select 'similarity atom pair' under 'Search Type', paste the following structure string into the SMILES field and search the 'ChemBridge 10K Microformat' database.













Demo Cheminformatics Workbench

To start an analysis on ChemMine's Cheminformatics Workbench, click on the side panel 'Manage CMPs' and then 'Add SMILES'. After this copy and paste the SMILES strings from below into the proper window. By clicking the 'Cluster' menu on the side panel of the ChemMine interface, the compounds can be clustered with different methods. The default settings are recommended for testing purposes. Similarly, the physicochemical descriptors can be computed for custom compound sets by clicking the 'Descriptors' option on the side panel. In addtition, the workbench allows users to view any combination of compounds in batches and to interconvert between different structure formats by clicking the different 'Download' options.

Compounds from Surpin et al (2005) in SMILES format: 
	P(Oc1ccccc1)(Oc1ccccc1)(=O)C	5135414
	n1c2c(ccc(c2)Nc2ccccc2)nc2c1cccc2	5271050
	C(Nc1ccc(cc1)Cl)(=O)COc1ccc(cc1)Cl	5320396
	c12cc(NC(=O)COc3cc(C)c(cc3)Cl)ccc1OCO2	5363833
	[N+](c1c(NC(=O)COc2ccc(cc2)Cl)cccc1)([O-])=O	5403629
	c1(c(n(c2ccccc2)n(c1C)C)=O)NC(c1cc(Cl)c(cc1)Cl)=O	5549214
	c1(sc(SCC)nn1)NC(c1oc(Br)cc1)=O	5694085
	c1(oc(\C=C\C(=O)O)cc1)c1cc(Cl)c(cc1)Cl	5850247
	O=Cc1ccc(OCc2ccc(cc2)F)cc1	5900360
	c1(c(ccc(c1)C)C(C)C)OCCNC(Cc1c2c(cccc2)ccc1)=O	5929549
	C(Nc1cc(C)c(cc1)C)(=O)COc1ccc(cc1)C	5940365
	c1c(N(C)C)cccc1NC(=O)CCc1ccccc1	6054314
	n1(c(nnc1C)C)\N=C\c1cc2c3c(cccc3)n(c2cc1)CC	6067962
	n1(C(c2c(ccc(c2)Cl)Cl)=O)c(nc2c1cccc2)C	6097727
	c1(nc(C)c2c(n1)cccc2)SCC(=O)OCC	6099904
	c1(nc(c2ccccc2)c(s1)C)NC(c1c([N+]([O-])=O)cccc1)=O	6100411
	N1(N=C(c2ccc(cc2)C)C[C@@H]1c1cc(OC)c(cc1)OC)C(=O)C	6110182
	n1(nc(C)cc1C)C(CNC(=O)COc1c(C)cccc1)=O	6123583
	C(Nc1ccc(cc1)Cl)(NCc1ncccc1)=O	6124497
	n1c(noc1COc1cc(C)c(cc1)Br)c1ccncc1	6126152
	C(Nc1cc(C(=O)C)ccc1)(=O)COc1ccc(cc1)OC	6138949
	C(=O)(NCC=C)COc1cc2ccccc2cc1	6139453
	N(C(=O)COc1cc2ccccc2cc1)c1c(CC)cccc1	6139547
	N(C(=O)COc1cc2ccccc2cc1)c1ncc(cc1)Cl	6141988
	c1(c(c2CCCc2s1)C(=O)OC)NC(=O)COc1c(cc(cc1)Cl)C	6145308
	C(=[NH]\OC(=O)COc1cc2ccccc2cc1)(\c1ncccc1)N	6149377
	o1c2cc(O[C@@H](C(=O)OC)C)ccc2ccc1=O	6155336
	N1(C(COc2cc3ccccc3cc2)=O)CCC(C(=O)OCC)CC1	6157413
	c1c([nH]nc1c1cc(C)ccc1)NC(=O)C	6160287
	C(Nc1ccncc1)(=O)COc1cc2ccccc2cc1	6162761
	c1(NC(=O)COc2cc3ccccc3cc2)c(c(C)ccc1)C	6163281
	S(c1ccc(cc1)C)(=O)(=O)NCCC(Nc1ccc([N+]([O-])=O)cc1)=O	6164506
	N1(c2cc(C(OCC(=O)c3ccccc3)=O)ccc2)C(CCC1=O)=O	6220480
	N1(C(CC(CC1(C)C)O)(C)C)C[C@@H](COc1c(cc(cc1)C)C)O	6241121












JOELib Descriptors

The following JOELib descriptors are generated and searchable in ChemMine: 

	MW: Molecular weight (MW)
	LGP: Octanol/Water partition coefficient (logP)
	HA1: Number of Hydrogen Bond Acceptors (HBA) 1
	HA2: Number of Hydrogen Bond Acceptors (HBA) 2
	HD1: Number of Hydrogen Bond Donors (HBD) 1
	HD2: Number of Hydrogen Bond Donors (HBD) 2
	ACG: Number of acidic groups
	AOH: Number of aliphatic hydroxy groups
	ARB: Number of aromatic bonds
	BAG: Number of basic groups
	FRB: Fraction of rotatable bonds
	ROT: Number of rotatable bonds
	HB: Number of heavy bonds
	HCY: Number of heterocycles
	HPG: Number of hydrophobic groups
	MR: Molar refractivity (MR)
	AT: Number of atoms
	HAL: Number of halogen atoms
	B: Number of boron atoms
	Br: Number of bromine atoms
	BON: Number of bonds
	Cl: Number of chlorine atoms
	I: Number of iodine atoms
	F: Number of fluorine atoms
	N: Number of nitrogen atoms
	O: Number of oxygen atoms
	P: Number of phosphorus atoms
	S: Number of sulfur atoms
	NO2: Number of -NO2 groups
	OSO: Number of -OSO atoms
	POL: Polar surface area (PSA)
	SO: Number of -SO groups
	SO2: Number of -SO2 atoms
	GDI: Geometrical diameter
	GRA: Geometrical radius
	GSH: Geometrical shape coefficient
	GRA: Graph shape coefficient
	TDI: Topological diameter
	TRA: Topological radius
	KS1: Kier Shape 1
	KS2: Kier shape 2
	ZI1: Zagreb index 1
	ZI2: Zagreb index 2