chemdb.ics.uci.edu

ChemDB Web Interface Index

Generate 2D images from SMILES. Convert between molecule file formats. Count functional groups (sub-structures). Screen molecules by functional group count. Fragment molecules for mass spec analysis. Search ChemDB by monoisotopic mass and substructure filtering. Predict activities of small molecules against a large set of protein targets. Datasets for training and testing machine learning and other algorithms. Relevant scientific articles published by our team. 23, 2348-2351 (2007). Learn and practice re...

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ChemDB Web Interface Index | chemdb.ics.uci.edu Reviews

<META> DESCRIPTION

Generate 2D images from SMILES. Convert between molecule file formats. Count functional groups (sub-structures). Screen molecules by functional group count. Fragment molecules for mass spec analysis. Search ChemDB by monoisotopic mass and substructure filtering. Predict activities of small molecules against a large set of protein targets. Datasets for training and testing machine learning and other algorithms. Relevant scientific articles published by our team. 23, 2348-2351 (2007). Learn and practice re...

<META> KEYWORDS

1 tools

2 smi2depict

3 babel

4 reaction processor

5 generate product libraries

6 pattern match counter

7 pattern count screen

8 msfragment

9 mass2structure

10 protein target predictor

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ChemDB Web Interface Index | chemdb.ics.uci.edu Reviews

https://chemdb.ics.uci.edu

Generate 2D images from SMILES. Convert between molecule file formats. Count functional groups (sub-structures). Screen molecules by functional group count. Fragment molecules for mass spec analysis. Search ChemDB by monoisotopic mass and substructure filtering. Predict activities of small molecules against a large set of protein targets. Datasets for training and testing machine learning and other algorithms. Relevant scientific articles published by our team. 23, 2348-2351 (2007). Learn and practice re...

INTERNAL PAGES

chemdb.ics.uci.edu

1

Supplementary Materials

http://chemdb.ics.uci.edu/cgibin/Publications.py

An Adaptive Reference Point Approach to Efficiently Search Large Chemical Databases. Francesco Napolitano, Roberto Tagliaferri, Pierre Baldi Recent Advances of Neural Network Models and Applications Smart Innovation, Systems and Technologies. 26, 63-74, (2014). Small-molecule 3D Structure Prediction Using Open Crystallography Data. P Sadowski and P. Baldi Journal of Chemical Information and Modeling. 53, 12, 3127-3130, (2013). A Unifying Kinetic Framework for Modeling Oxidoreductase Catalyzed Reactions.

2

ReactionProcessor: SMIRKS Based Product Library Generation

http://chemdb.ics.uci.edu/cgibin/reaction/ReactionProcessorWeb.py

ReactionProcessor: SMIRKS Based Product Library Generation. SMI - SMILES, Absolute. CAN - Canonical SMILES. ISM - Isomeric SMILES. SDF - MDL SD File. MDL - MDL Mol File. MOL2 - Tripos Sybyl mol2 file. MOL2H - Sybyl mol2 with explicit hydrogens. PDB - Protein Databank PDB file. BIN - Old Style OEBinary. MF - Molecular Formula (Hill order). XYZ - XMol XYZ format. FASTA - FASTA protein sequence. MOPAC - MOPAC file format(s). OEB - New Style OpenEye OEBinary. SMI - SMILES, Absolute. CAN - Canonical SMILES.

3

Smi2Depict: Generate 2D Images from Molecule Files

http://chemdb.ics.uci.edu/cgibin/Smi2DepictWeb.py

Smi2Depict: Generate 2D Images from Molecule Files. C1ccccc1O CCCCN 0 NC(O)C(=O)O 1 CCCCO 2 CCCCC(=O)O 3 OCCCCCN 4 O/C=C N 5 CC=CC(=O)O 6 OCC[C@H](O)CC 7.

4

Database Download

http://chemdb.ics.uci.edu/cgibin/supplement/Download.py

Download: All Chemical Isomers. All of the chemical isomers in the database are available for download, including all of their primary chemical annotations. They are available for download as a collection of gzipped SDF molecular format files, each about 100 MB large. Note that small subsets of chemicals and isomers are available for download based on specific search criteria are via the ChemicalSearch. First and we may be able to provide a stripped down "raw" version of the data for you.

5

ReactionMap: predict the mapping of reactant atoms to product atoms

http://chemdb.ics.uci.edu/cgibin/reactionmap/ReactionMapWeb.py

ReactionMap: predict the mapping of reactant atoms to product atoms.

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Tools & Databases

http://www.igb.uci.edu/tools.html

Skip to main navigation. Skip to first column. Skip to second column. The Institute provides a number of services for universities, companies, and other organizations and has developed widely used databases. Software, and web servers in chemoinformatics. The UCI Genomics High-Throughput Facility. Provides genome-wide analysis for clients interested in gene expression, regulation of gene expression, and genome sequence and variation.

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ChemDB Web Interface Index

Generate 2D images from SMILES. Convert between molecule file formats. Count functional groups (sub-structures). Screen molecules by functional group count. Fragment molecules for mass spec analysis. Search ChemDB by monoisotopic mass and substructure filtering. Predict activities of small molecules against a large set of protein targets. Datasets for training and testing machine learning and other algorithms. Relevant scientific articles published by our team. 23, 2348-2351 (2007). Learn and practice re...

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