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MaizeGDB External Resources
Bioinformatics, Biochemistry, and Metabolic Resources

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Biochemistry and Metabolism

American Chemical Society Publications
http://pubs.acs.org
This site provides articles and resources for all of the publications of the American Chemical Society.

IUPAC (International Union of Pure and Applied Chemistry) Naming Conventions
http://www.chem.qmw.ac.uk/iupac
This site contains the full text of all naming conventions for chemicals, as developed by IUPAC.

Journal of Molecular Modeling
http://www.ccc.uni-erlangen.de/jmolmod/
The Journal of Molecular Modeling is a fully archived electronic and print journal on molecular modeling.

KEGG: Kyoto Encyclopedia of Genes and Genomes
http://www.genome.ad.jp/kegg/
A grand challenge problem in the post-genomic era is a complete computer representation of the cell and the organism, which will enable in silico analysis of higher order cellular functions and organismic behaviors. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource challenging this problem by making use of large-scale data in genomics and proteomics.

MolBiol.net
http://www.molbiol.net/
MolBiol.net is an extensive and thorough collection of molecular biology resources.

PLACE: A Database of Plant Cis-acting Regulatory DNA Elements
http://www.dna.affrc.go.jp/htdocs/PLACE/
PLACE is a database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled.

PIR: Protein Information Resource
http://pir.georgetown.edu
PIR is an integrated public resource of protein informatics to support genomic and proteomic research and scientific discovery.

Simulation of Cell Processes - ECell
http://www.e-cell.org
E-Cell is a project devoted to collecting and maintaining resources related to the simulation of cellular processes.

WIT: What Is There? Interactive Metabolic Reconstruction on the Web
http://ftp.mcs.anl.gov/pub/tech_reports/reports/P694.html
WIT is a www-based system to support the curation of function assignments made to genes and the development of metabolic models.

Bioinformatics

The Biology Workbench @ SDSC
http://workbench.sdsc.edu/
The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.

BLOCKS
http://blocks.fhcrc.org
Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. The BLOCKS website is a service for biological sequence analysis.

EMBL: European Molecular Biology Laboratory
http://www.embl-heidelberg.de
The European Molecular Biology Laboratory hosts a great number of bioinformatics resources and tools.

ExPaSy / Swiss-Prot
http://us.expasy.org/
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.

NCGR: National Center for Genomic Research
http://www.ncgr.org/
NCGR creates biological databases and analytical tools to accelerate and enable discovery. Primary research areas include genomics, biochemical pathways and gene expression.

NCBI / GenBank
http://www.ncbi.nlm.nih.gov
NCBI creates public databases, conducts research in computational biology, develops tools for analysing genome data, and disseminates biomedical data. Among these resources are GenBank and PubMed.

NCBI dbEST
http://www.ncbi.nlm.nih.gov/dbEST/index.html
dbEST is a division of GenBank that contains sequence data and other information on expressed sequence tags for a number of organisms.

PlantGDB: Plant Genome Database
http://www.plantgdb.org
PlantGDB is a NSF-funded project intending [1] to set up annotated species-specific EST databases for all major plants and link the EST data to other biological information, [2] to establish inter-species query capabilities to allow cross-species comparisons, and [3] to provide web-accessible computational tools for gene identification and characterization.


Many thanks to Ed Coe and Mary Polacco for collecting and providing many of the URLs used here.

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Last updated 1:50 pm, Dec 03, 2014.

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