CHEMISTRY RESEARCH
Evangel University Library Staff
2016
NOTE: any link marked as a PORTAL offers many useful links itself.
Part I: General Searching:
General searching online may be greatly focused by using Google Scholar.
It may even be focused more by using these simple aids: 1) add “site:edu” to limit all search results to those associated with a college or university, plus high schools, in the United States, or, “site:ac” for those outside the US; 2) add: intitle:”selenium oxide” to find all papers where a word or phrase is so important within the paper that it is included in the title of the paper.
To focus/limit a search go to www.about.com and make a search for Search Engine Cheat Sheets. There are shortcuts for Google, Bing, Ask, Yahoo, etc. DuckDuckGo has focused searching, too. Its link to shortcuts is: http://websearch.about.com/od/enginesanddirectories/p/Duckduckgo.htm.
For future searches for newer / better resources, make searches similar to: Chemistry Portals and Chemistry Directories. With these, you will be using the research findings of outstanding associations, colleges, universities, and corporate researchers who seek or develop the best aids available.
Niche/speciality search engines are invaluable. Watch for them within the portals and/or directories.
Using Proximity Searching hints you can limit how far apart two or more words may appear in a document and their order. To search Google, use First Word * Second Word to limit two words or phrases to being located within 2 or perhaps 3 words of each other. Add another asterisk to broaden the distance between words or phrases. Also, Google permits searches using this pattern: First word AROUND3 Second Word to locate words within 3 words of each other (number may be changed). To made a Proximity search in Bing.com use the search: First Word near:3 Second Word (or change number to narrow or broaden the search).
Citation Searching as a specialized search: a number of databases (including Google Scholar) offer ways to look for articles & books cited in a work, i.e., its bibliography, and to search for sources which have themselves subsequently cited it. This can be an exacting search. Not all databases offer it but subject researchers expected to do a literature search, or a search demonstrating the expansion and development of ideas and concepts within the literature of a genre, should look at the Help Screens or a Tutorial for each database to find methods.
NO MATTER YOUR BACKGROUND:
When you use a new database, please look at its Help or Tutorial link and see how it does the following:
Truncation (*, ?, $); Proximity searching; Nested or Boolean searching; Limiting; Field searching; and its Advanced Search’s “bells and whistles” .
Part II: Do not yet have a citation or source?
Major sources:
Open Science Directory http://www.opensciencedirectory.net/ Especially note its programs: HINARI, AGORA, INASP-PERI, OARE, eIFL and eJDS available through Research 4 Life: Access to Research in the Developing World. Access up to 69,000 scientific journals, books and databases http://www.research4life.org/ .
Free Online Scientific Resources - External (CDS National Chemical Database Service (Royal Society of Chemistry)) http://cds.rsc.org/externalresources.asp Portal.
PubChem: [National Center for Biotechnology Information, US National Library Of Medicine freely available database] http://pubchem.ncbi.nlm.nih.gov/ “ It consists of three databases (PubChem BioAssay, PubChem Substance, and PubChem Compound) linked together in the Entrez information retrieval system of the National Center for Biotechnology Information (NCBI).”
PubChem YouTube Tutorial http://www.youtube.com/watch?v=piYf5QfJ8OM . Other related videos may also be viewed.
PubChem Help /print tutorial is available at http://pubchem.ncbi.nlm.nih.gov/help.html . “This
document provides tips and examples for searches on the three PubChem databases by text
term/keyword, as well as tips for searching PubChem Compound by chemical properties.”
A longer overview of PubChem may be found at
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703903/ .
See http://www.infotoday.com/online/sep07/Baykoucheva.shtml for an aditional detailed explanation of PubChem.
PubMed (US Nat. Lib. of Medicine. National Institutes of Health) http://www.ncbi.nlm.nih.gov/pubmed The largest collection of medical articles. [See PubMed Central below for the FREE full text articles in PubMed.] PubMed Tutorial (US National Library of Medicine. National Institutes of Health) http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/015_010.html At the end of the tutorial it says, “…you have seen the Related Citations feature and for LinkOut. This section discusses the links from PubMed that take you to other NCBI resources. [Now] See an interactive view of Entrez links at http://www.ncbi.nlm.nih.gov/Database/” and continue to the next page. (About 17-20% of the content is free..)
PubMed Central (PMC) http://www.ncbi.nlm.nih.gov/pmc/ PMC is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.
EUROPEAN PubMed Central (UK and Europe) http://europepmc.org/ Based on PubMed Central (PMC), the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.
Chemistry Central: open access to chemistry “(www.chemistrycentral.com) launched by BioMed Central in 2006.
Chemical Portal (WebQC.Org)( Vitalii Vanovschi) http://www.webqc.org/ and Online Chemical Tools http://www.webqc.org/chemicaltools.php . [Please use left ribbon to explore Chemical Portal in depth.]
Organic Chemisty Portal http://www.organic-chemistry.org/chemicals/search.htm
Links for Chemists (Combinatorial Chemistry Review) http://www.combichemistry.com/links.html.
Resources for Teaching Chemistry http://www.csun.edu/science/chemistry/
BASE (Bielefeld Academic Search Engines) (Germany) http://www.base-search.net/ “BASE is one of the world's most voluminous search engines especially for academic open access web resources.”
Wolfram Alpha: The Computational Search Engine www.wolframalpha.com Includes: Chemical Names and Formulas; Structure diagram; 3D structure; Basic properties; Liquid properties (at STP); Thermodynamic properties; Chemical identifiers; NFPA label; Safety properties; and Toxicity properties. Chemistry widget: http://www.wolframalpha.com/widgets/gallery/?category=chemistry .
Science Search Tools: Government databases http://www.osti.gov/home/scienceinfo
Chemistry Directories:
1. Chemistry Directory (Open Directory Project http://www.dmoz.org/Science/Chemistry/
2. Best of the Internet http://www.botid.org/Science/Chemistry/ Note disiplines on the left ribbon.
Chemical Thesaurus http://www.chemthes.com/
Chemistry Portals:
Examples of a good portal (a “doorway” to knowledge about a specific topic) are:
1. Chemistry Guide http://www.chemistryguide.org/ Covers Websites in 23 broad subjects. (See also Links for Chemists above.) Portal.
2. CWM Global Search: The Internet Search Engine for chemists and biologists http://www.akosgmbh.de/globalsearch/index.htm Portal.
3. iScienceSearch http://isciencesearch.com/iss/ “Search by structure, text, name and identifiers in 100 chemical and biological databases.” Portal.
4. Chemical Information Sources/SIRCh Selected Internet Sources for Chemistry (Wikibooks) https://en.wikibooks.org/wiki/Chemical_Information_Sources/SIRCh Portal.
5. Chemisty and related information on the Internet (Department of Chemistry. University of Oxford) http://www.chem.ox.ac.uk/cheminfo/internet.html Portal.
6. Chemistry: Internet Resources (A. Ben Wagner. University Libraries. University at Buffalo, SUNY) http://libweb.lib.buffalo.edu/guide/guide.asp?ID=146 Portal.
Part III: More Specialized Resources:
ChemXSeer: (Penn State University & National Science Foundation) http://chemxseer.ist.psu.edu/ The Help pages for ChemXSeer: http://chemxseer.ist.psu.edu/ChemXSeerFormulaSearch/help.htm
ChemNet: http://my.rsc.org/chemnet/resources .The Royal Chemisty Society (RCS)
World Wide Science Search Engine: Global Science Gateway http://worldwidescience.org/
It includes “… federated searching of national and international scientific
databases and portals.”
Textbooks:
Chem 1 Virtual Textbook (Stepen Lower). (Simon Fraser University, Can.)
http://www.chem1.com/acad/webtext/virtualtextbook.html
ChemWiki: the Dynamic Chemistry Textbook http://chemwiki.ucdavis.edu/
Organic Chemistry Toolkit (Bob Hanson) (St. Olaf College)
http://www.stolaf.edu/depts/chemistry/courses/toolkits/247/
Virtual Chemistry Textbook (About.com Education) http://chemistry.about.com/od/virtualchemistrytextbook/Virtual_Chemistry_Textbook.htm
Virtual Textbook of Organic Chemistry (Michigan State University) (William Reusch.) http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/intro1.htm
Handbooks:
Chemistry and Physics Handbooks Online Free (Genres on left)
http://ebookmarket.org/doc/chemistry-and-physics-handbook-online-free
Laboratory Chemistry Books http://freebookcentre.net/Chemistry/Laboratory-Chemistry-Books.html
NIST (National Institute of Standards and Technology) Chemistry WebBook. NIST Standard Reference Database Number 69 http://webbook.nist.gov/chemistry/
NIOSH Pocket Guide to Chemical Hazards http://www.cdc.gov/niosh/npg/
Solving Problems: A Chemistry Handbook
http://teacherweb.com/GA/NorthPauldingHighSchool/TBrown/spcmc.pdf
Dictionary:
ChemIDPlus Advanced (National Library of Medicine) (TOXNET database)
http://chem.sis.nlm.nih.gov/chemidplus/
ChEBI: Chemical entities of biological interest (EMBL-EBI, European
Bioinformatics Institute) http://www.ebi.ac.uk/chebi/
Chemistry Dictionary and Glossary http://www.chemistry-dictionary.com/
Croation-English Chemistry Dictionary and Glossary (Inorganic Chemistry) http://glossary.periodni.com/glossary.php?en=inorganic+chemistry
General Chemistry Dictionary (Fred Senese)
http://chemistry.science-dictionary.org/General-Chemistry-Dictionary/
Encyclopedia:
Eric Weisstein’s World of Chemistry (Wolfram Research) http://scienceworld.wolfram.com/chemistry/
Chemistry: A to Z Index (About.com) (Anne Marie Helmenstine, Ph.D., About.com Guide)
http://chemistry.about.com/od/chemistryatoz/Chemistry_A_to_Z_Index_Encyclopedia_of_Chemistry.htm
Encyclopedia 4U: Chemistry www.encyclopedia4u.com/c/chemistry.html
Encyclopedia of Chemistry
http://chemistry.about.com/od/chemistryatoz/Chemistry_A_to_Z_Index_Encyclopedia_of_Chemistry.htm
Chemistry: Wikipedia [use with caution] http://www.wikipedia.org/chemistry and its related links.
Affinity:
PDBBind http://sw16.im.med.umich.edu/databases/pdbbind/index.jsp (2007 release) The 2012
release is available at http://sw16.im.med.umich.edu/databases/pdbbind/index.jsp
AffinDB: affinity database for protein-ligand complexes
http://pc1664.pharmazie.uni-marburg.de/affinity/index.php Help Screen:
http://pc1664.pharmazie.uni-marburg.de/affinity/help.php
Allergies and Infectious Diseases:
National Institute of Allergy and Infectious Diseases Database http://chemdb.niaid.nih.gov/ . “ http://chemdb.niaid.nih.gov/memo/dmid-ls-113.aspx
Help Screen: http://chemdb.niaid.nih.gov/help/Help.aspx
Analytical Chemistry:
Analytical Chemistry Links (Vitual Library) http://www.liv.ac.uk/Chemistry/Links/refanal.html A Portal.
Analytical Chemistry Springboard (Umeå University) http://www.anachem.umu.se/Jumpstation.htm A Portal.
Biochemistry:
AGRICOLA http://agricola.nal.usda.gov/help/aboutagricola.html
BASE (Bielefeld Academic Search Engine) (Germany) http://www.base-search.net/ “BASE is one of the world's most voluminous search engines especially for academic open access web resources.”
BiGG (University of California at San Diego) http://bigg.ucsd.edu/
Biochemical Pathways Database under C@ROL (BioPath) (University of Erlangen)
http://www2.chemie.uni-erlangen.de/services/biopath/
BioGRID http://thebiogrid.org/index.php (Biological General Repository for Interaction
Datasets)
Biological Macromolecule Crystallization Database, BMCD
http://xpdb.nist.gov:8060/BMCD4/index.faces It
Biological Magnetic Resonance Data Bank, BioMagResBank, BMRB http://www.bmrb.wisc.edu/
BioMeta Database (CMBI) http://biometa.cmbi.ru.nl/ “..based on the KEGG Ligand database
http://www.genome.jp/ligand/ “. (Updated 2012)
Biopath.Explore (Molecular Networks, Germany) https://webapps.molecular-networks.com/biopath3/
Biopharmaceutical Products in the U.S. and European Markets http://www.biopharma.com/
Biophysical Chemistry Databases (University of Massachusetts Library) (Look for free databases)
http://www.chem.umass.edu/~cmartin/CTMWEBLinks/AnnMcD's%20Biophys%20Sites.html
NetPhosK 1.0 Server http://www.cbs.dtu.dk/services/NetPhosK/
Bordwell pKa Table (Acidity in DMSO) (University of Wisconsin) “Copyright 2001-2012 Hans J.
Reich. All Rights Reserved.” http://www.chem.wisc.edu/areas/reich/pkatable/
Biochemistry: Open Access Resources (Helen B. Helm) http://www.pages.drexel.edu/~hlh44/final/databases.html A Portal.
Biochemistry Pathways Database under C@ROL (TORVS Research Team : Techniques for Organic
Reactions, Visualization and Spectrosopy)
http://www2.chemie.uni-erlangen.de/services/biopath/index.html
BioText Search Engine (UC-Berkeley) http://biosearch.berkeley.edu/ “Search more than 300
CEBS, Chemical Effects in Biological Systems
http://www.niehs.nih.gov/research/resources/databases/cebs/index.cfm
Flexweb; Analysis of Flexibility in Biomolecules and Networks (Arizona State University)
GreenFILE (EBSCO) www.greeninfoonline.com
Indiana University Molecular Structure Center (Reciprocal Net. Indiana University)
http://bl-chem-iumsc110.chem.indiana.edu/recipnet/search.jsp
Medical Biochemistry Page (MedEd Portal) http://themedicalbiochemistrypage.org/index.php
NetBioChem (James Baggott and Sharon E. Dennis) (NLM) http://library.med.utah.edu/NetBiochem/ A
Portal.
Proton NMR Spectra of Xyloglucans and, GC-EIMS of Partially Methylated Alditol Acetates
http://www.ccrc.uga.edu/specdb/specdbframe.html
Science.gov http://www.science.gov/ “Science.gov searches over 60 databases and over 2200 selected websites from 15 federal agencies.” Chemistry Sources at Science.gov
http://www.science.gov/browse/w_129A.htm
Scitable: a collaborative learning space for science (Nature Education. Nature Publishing Group) http://www.nature.com/scitable
North Carolina BioGrid http://www.ncbiogrid.org/ and: PRAGMA (Pacific
Rim researchers) http://www.pragma-grid.net/benefits.php
ToxLine (National Library of Medicine. ToxNet: Toxicolopgy Data Network. Toxicology Literature Online)
http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?TOXLINE
Bioinformatics:
GridFTP Glycan Database
http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp
glycoSCIENCES.DE http://glycosciences.de/
I-ChemiSt, Intelligent Chemical Structural Database (Mass spectroscopy and NMR spectra databases) (San Diego State University) http://bioinformatics.sdsu.edu/research.php
Life Science Gateway http://www.globus.org/solutions/olsgw/ A Portal.
OBRC; Online Bioinformatics Resources Collections http://www.hsls.pitt.edu/obrc/
Nucleic Acids Research Molecular Biology Database Collection http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531151/
SPECARB, Raman spectra of carbohydates http://www.models.life.ku.dk/~specarb/
Sung Kwang’s Cheminformatics & Molecular Modeling Weblinks http://www.qspr.pe.kr/my/index.php?option=com_bookmarks&Itemid=10 A Portal.
Chemical Genetics:
ChemBank: Initiative for chemical genetics http://chembank.broadinstitute.org/
Enhanced NCI Database Browser (University of Erlangen) http://cactus.nci.nih.gov/ncidb2.2/
Chemical Reactions:
Chemogenesis Web Book Videos http://www.meta-synthesis.com/webbook/90_videos/videos.html
Reaction Database (Sigma Aldrich)
http://www.sigmaaldrich.com/help-welcome/product-search/reaction-database.html
Chemicals:
ChemFinder (CambridgeSoft; requires plugin for substructure searching)
http://www.cambridgesoft.com/databases/login/?serviceid=128
Chemical Acronyms Database (maintained by the Indiana University Chemistry Library)
http://bl-libg-doghill.ads.iu.edu/chem-web/databases/acronyms/index.php
Chemical Information Sources http://en.wikibooks.org/wiki/Chemical_Information_Sources A Portal.
Chemicalize.org http://www.chemicalize.org/
Chemical Space Project http://reymond.dcb.unibe.ch/research/research.html
Chemical Structure Lookup Service (CSLS): a database locator service
http://cactus.nci.nih.gov/cgi-bin/lookup/search
Atomic Reference Data for Electronic Structure Calculations
http://www.nist.gov/pml/data/dftdata/index.cfm
ChemSynthesis Chemical Database http://www.chemsynthesis.com/
ChemExper http://www.chemexper.com/
Common Chemistry (CAS) http://commonchemistry.org/
Help Screen: http://commonchemistry.org/help.aspx
Chemical Identifier Resolver beta 4 http://cactus.nci.nih.gov/chemical/structure
ChemSpider : the free chemical database (Royal Society of Chemistry) http://www.chemspider.com/
Help Screen: http://www.chemspider.com/Help.aspx
Also accessible:
ChemSpider Synthetic Pages http://cssp.chemspider.com/ Help Screen: on top ribbon
ChemSpider InChIs Resolver http://www.chemspider.com/inchi-resolver/
Envirofacts Master Chemical Integrator (EMCI) (US EPA)
http://www.epa.gov/enviro/html/emci/chemref/
PheroBase: database of pheronones and semiochemicals http://www.pherobase.com/
Chemicals for Purchase:
ChemIndustry http://www.chemindustry.com/index.html
Zinc (University of California, San Francisco): free database of over 21 million purchasable
compounds in ready-to-dock, 3D formats-available for virtual screening
Molport: Buy chemicals. We get Molecules Delivered http://www.molport.com/buy-chemicals/index
InternetChemistry.com: … to the world of chemistry
http://www.internetchemistry.com/chemistry-index.html
Query Chem http://llama.mshri.on.ca/~jklekota/QueryChem.html
Chemistry Guide:
Chemistry, Synthetic:
ChemSpider Synthetic Pages http://cssp.chemspider.com/browse.aspx See YouTube for ChemSpider
Synthetic Pages tutorials.
Synthetic Chemistry Pages http://www.syntheticpages.org/
ChemDB, the UC Irvine ChemDB http://cdb.ics.uci.edu/ Cheminformatics Portal
Overview of datasets: http://cdb.ics.uci.edu/cgibin/LearningDatasetsWeb.py
Offers: “Molecules: ChemicalSearch; Virtual Chemical Space; MOLpro; AquaSol; COSMOS; Tools:
Smi2Predict;Babel; Reaction Processor; Pattern Match Counter; Pattern Count Screen;
MSFragment; Mass2Structure; Datasets (see link above); Reactions: Reaction Explorer; Reaction
Predictor.”
MedChem/Biobyte QSAR Database (Pomona College) http://www.cqsar.com/medchem/chem/qsar-db/
Sung Kwang’s Cheminformatics & Molecular Modeling Weblinks http://www.qspr.pe.kr/my/index.php?option=com_bookmarks&Itemid=10 A Portal. [Over 900 pages of links]
Computations:
Chemputer (Sheffield University) http://winter.group.shef.ac.uk/chemputer/
Wolfram Alpha chemistry computations
http://www.wolframalpha.com/input/?i=chemistry+computations
Crystallography:
American Mineralogist Crystal Structure Database http://www.nist.gov/pml/data/dftdata/index.cfm
CrystalEye (beta) (University of Cambridge) http://wwmm.ch.cam.ac.uk/crystaleye/
Drugs:
DrugBank: Open Data Drug * Drug Target Database http://www.drugbank.ca/ Help Screen: located
on top ribbon.
P450 (Cytochrome) Drug Interaction Table (School of Medicine, Indiana University. Division of Clinical
Pharmacology) http://medicine.iupui.edu/clinpharm/DDIs/table.aspx
National Drug Code Registry (U.S. Food and Drug Administration): Protecting and Promoting Your Health
http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm
ChemInformatic Tools and Databases http://chemoinfo.ipmc.cnrs.fr/MOLDB/index.html
Pharmabase: a database of cellular physiology & pharmacology http://www.pharmabase.org/
NIMH Psychoactive Drug Screening Program (PDSP) http://pdsp.med.unc.edu/indexR.html
Drugable.com: Bioactivity simplified http://drugable.com/ “ … a comprehensive index of druggable
small molecule chemistry and protein targets.” Help Screen: http://drugable.com/help
Enzymes:
BRENDA http://www.brenda-enzymes.org/ It has a Tutorial.
CAZy, Carbohydrate-Active enZymes http://www.cazy.org/
MetaCyc: a member of the BioCyc database collection http://metacyc.org/ Help Screen: on top ribbon.
Formulas, Chemistry:
Species Data by Chemical Formula http://webbook.nist.gov/chemistry/form-ser.html
Wolfram Alpha Chemistry Formulas http://www.wolframalpha.com/input/?i=chemistry+formulas
eggNOG, version 3.0 (Germany) http://eggnog.embl.de/version_3.0/ “ Help Screen:
http://eggnog.embl.de/version_3.0/help.html
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) (Germany): Known and Predicted Protein-Protein Interactions http://string.embl.de/ Help Screen:
http://string.embl.de/newstring_cgi/show_info_page.pl?UserId=BAfz_p8pUeS5&sessionId=jWwGDgMuz653
Informatics:
ChemDB, the UC Irvine ChemDB http://cdb.ics.uci.edu/ Cheminformatics Portal. Molecules; Tools;
Reactions; Datasets; Chemical Isomers; Analysis.
Reactome, a curated knowledgebase of biological pathways
http://www.reactome.org/ReactomeGWT/entrypoint.html It is “… cross-referenced to many bioinformatics databases. These include NCBI Entrez Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology, ChEBI, PubMed and GO.”
Inorganic:
SitesBase http://www.modelling.leeds.ac.uk/sb/
Therapeutic Target Database http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp
Lipids:
Medical Subject Headings, MeSH (US National Library of Medicine)
http://www.nlm.nih.gov/mesh/meshhome.html MeSH is a controlled vocabulary thesaurus.
MEDPHYT (The Medicinal Plants Database) http://www.pfaf.org/user/plantsearch.aspx
Metabolome / Metabolites:
Human Metabolome Database (University of Alberta, Canada) http://www.hmdb.ca/ “ Four additional
databases, DrugBank, T3DB, SMPDB and FooDB are also part of the HMDB suite of databases.”
Golm Metabolome Database (Germany) http://gmd.mpimp-golm.mpg.de/ Help Screen:
http://gmd.mpimp-golm.mpg.de/help.aspx
Metlin Metabolite Database http://metlin.scripps.edu/
METLIN: Metabolite and Tandem MS Database (Scripps Center for Metabolomics) http://metlin.scripps.edu/
Modeling, Chemical:
Online chemical database with modeling environment https://www.ochem.eu/home/show.do
Molecules (Including Genomes): (See also Compounds, Molecules above)
BioCyc Database Collection http://biocyc.org/intro.shtml Help Screen: located on top ribbon
Calculation of Molecular Properties and Drug-Likeness (Molinspiration)
http://www.molinspiration.com/cgi-bin/properties
eMolecules: Linking researchers needs to supplier capabilities http://www.emolecules.com/
Help Screen: http://www.emolecules.com/doc/basic-chemical-search.php
JURISICA Lab: IBM Life Sciences Discovery Center http://www.cs.toronto.edu/~juris/home.htm
Computational Chemistry Comparison and Benchmark DataBase http://cccbdb.nist.gov/
ChemMine (University of California – Riverside) http://chemmine.ucr.edu/ Help Screen:
http://chemmine.ucr.edu/iframe/work/intro/tutorial
BindingDB http://www.bindingdb.org/bind/index.jsp Search Screen: Tutorials located on home page
DockBlaster (Shoichet Laboratory, University of California – San Francisco) http://blaster.docking.org/
Help Screen: Frequent Questions and Examples of Use located in main menu
Generated Database of Chemical Universe of Small Molecules (Chemical Space Project) (Germany)
http://www.dcb.unibe.ch/groups/reymond/ (The German site is consistently given as the
originator: http://www.dcb.unibe.ch/content/index_eng.html.)
HIC-Up, Hetero-compound Information Centre, Uppsala http://xray.bmc.uu.se/hicup/
OpenMolecule.org http://www.openmolecules.org/
STITCH 3.1 (Germany) http://stitch.embl.de/ Help Screen:
http://chemmine.ucr.edu/iframe/work/intro/tutorial
RCSB PDB: Protein Data Bank {Rutgers) http://www.rcsb.org/pdb/home/home.do “... portal to Biological
Macromolecular Structures”
Help Screen: http://www.rcsb.org/pdb/static.do?p=general_information/screencasts.jsp
ChEMBLdb https://www.ebi.ac.uk/chembldb/ Help Screen: located on top ribbon
CoCoCo (Commercial Compound Collection) http://cococo.unibo.it/
KEGG: Kyoto Encyclopedia of Genes and Genomes http://www.genome.jp/kegg/ Help Screen:
http://www.genome.jp/kegg/document/help_kegg_search.html
KEGG API http://www.kegg.jp/kegg/rest/
KEGG pathway http://www.genome.jp/kegg/pathway.html
MolTable: An Open Access (Molecule Table) Portal for "Advanced Chemoinformatics Research, Training
and Services"
http://moltable.ncl.res.in/web/guest;jsessionid=2CCDCFB36A146D7CC8125E257DEE047C A
Portal.
SitesBase http://www.modelling.leeds.ac.uk/sb/
Sung Kwang’s Cheminformatics & Molecular Modeling Weblinks http://www.qspr.pe.kr/my/index.php?option=com_bookmarks&Itemid=10 A Portal. [Over 900 pages of links]
SureChem Open Patent Data (SureChEMBL) http://www.chemistryguide.org/chemical-databases.html
Symmetry@Otterbein University http://symmetry.otterbein.edu/ Help Screen:
http://symmetry.otterbein.edu/tutorial/index.html
Nanochemistry:
Nanochemistry http://www.internetchemistry.com/chemistry/nanochemistry.htm
NIST (National Institute of Standards and Technology) Resources:
IUPAC-NIST Solubility Database http://srdata.nist.gov/solubility/
NIST Chemistry WebBook (National Institute of Standards and Technology. U.S. Secretary of Commerce)
http://webbook.nist.gov/chemistry/
NIST Chemical Kinetics Database http://kinetics.nist.gov/kinetics/index.jsp Help Screen: on left ribbon
NIST Data Gateway http://srdata.nist.gov/gateway/
NIST Databases http://srdata.nist.gov/gateway/gateway?dblist=0
NIST Physics Laboratory Physical Reference Data (US National Institute for Standards and Technology)
http://www.nist.gov/pml/data/index.cfm
Nucleic Adics:
Nucleic Acids Database (Rutgers University: a repository of three-dimensional structural information
about nucleic acids) http://ndbserver.rutgers.edu/
Nucleic Acids Research Molecular Biology Database Collection http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531151/
Occupational Safety:
CAMEO Chemicals (NOAA) http://cameochemicals.noaa.gov/
CCOHS Web Information Service http://ccinfoweb.ccohs.ca/
Hazardous Substances (DMOZ) http://www.dmoz.org/Health/Occupational_Health_and_Safety/Hazardous_Substances/
Material Safety Data Sheets (MSDS) (DMOZ) http://www.dmoz.org/Health/Occupational_Health_and_Safety/MSDS/
NIOSH Databases and Information Resources (US National Institute for Occupational Safety and Health) http://www.cdc.gov/niosh/database.html
Organic:
CATH, Protein Structure Classification (Cath Gene3D: Clusters proteins at four major levels, Class(C),
Architecture(A), Topology(T) and Homologous superfamily (H)) http://www.cathdb.info/
Organic Databases (DMOZ) http://www.dmoz.org/Science/Chemistry/Organic/Databases/ A Portal.
Organic Syntheses: a publication of reliable methods for the preparation of organic compounds http://www.orgsyn.org/
e-EROS Electronic Encyclopedia of Reagents for Organic Synthesis
http://onlinelibrary.wiley.com/book/10.1002/047084289X
NMRShiftDB (Germany) http://nmrshiftdb.nmr.uni-koeln.de/ Help Screen: http://tinyurl.com/b78nce8
Mylims.org: My database of spectra and chromatograms http://mylims.epfl.ch/ Help Screen: on top
ribbon
NRG-CING (Netherlands) http://proteins.dyndns.org/cing/NRG-CING.html Help Screen:
http://proteins.dyndns.org/cing/Tutorials/Tutorials.html
Madison-Qingdao Metabolomics Consortium Database http://mmcd.nmrfam.wisc.edu/ Help Screen:
http://mmcd.nmrfam.wisc.edu/database_help.htm
SPECARB, Raman spectra of carbohydates http://www.models.life.ku.dk/~specarb/
SUGABASE, carbohydrate NMR database
http://glycomics.ccrc.uga.edu/GlycomicsPortal/showEntry.action?id=48
Patents:
Free Patents Online http://www.freepatentsonline.com/
Fresh Patents http://www.freshpatents.com/
Google Patent Search https://www.google.com/?tbm=pts&gws_rd=ssl
Japan Patent Office http://www.jpo.go.jp/index_e/patents.html
Lens (European Patent Office, Cambia) https://www.lens.org/lens/search
OWL, Composite Protein Sequence Database (Covers SWISS-PROT, PIR, GenBank, and NRL-3D)
http://www.bioinf.manchester.ac.uk/dbbrowser/OWL/index.php
Patent Buddy: About: http://www.patentbuddy.com/pages/aboutUs.jsf; Patent Buddy
Also, from the US Patent and Trademark Office: http://patft.uspto.gov/ Provides free access to the US
patent databases, EU patent databases (European Patent Office http://www.epo.org/ and
Resources for Foreign Patents
http://www.uspto.gov/web/patents/searchtemplates/class280-006_15.htm or use
PatentScope http://patentscope.wipo.int/search/en/search.jsf “Search International and
National Patent Collections”.
SureChem Open Patent Data (SureChEMBL) http://www.chemistryguide.org/chemical-databases.html
U.S. Patent and Trademark Office http://patft.uspto.gov/
World Intellectual Property http://www.wipo.int/reference/en/
Pesticides:
Compendium of Common Pesticide Names http://www.alanwood.net/pesticides/ Help Screen: Hints and Tips on main menu.
Pharmaceutical Chemistry:
Dr. Duke's Phytochemical and Ethnobotanical Databases http://www.ars-grin.gov/duke/
Proteins:
DIP (Database of Interacting Proteins) (UCLA)
http://dip.doe-mbi.ucla.edu/dip/Main.cgi
DisProt Database of Protein Disorder http://www.disprot.org/
Human Protein Reference Database http://www.hprd.org/
iHOP, information Hyperlinked Over Proteins http://www.ihop-net.org/UniPub/iHOP/
IntAct (Protein Interaction Database) http://www.ebi.ac.uk/intact/main.xhtml
MINT Molecular Interactions Database http://mint.bio.uniroma2.it/mint/Welcome.do
NAViGaTOR (University of Toronto) http://ophid.utoronto.ca/navigator/
OWL, Composite Protein Sequence Database (Covers SWISS-PROT, PIR, GenBank, and NRL-3D)
http://www.bioinf.manchester.ac.uk/dbbrowser/OWL/index.php
SCOP, Structural Classification of Proteins http://scop.mrc-lmb.cam.ac.uk/scop/
Structural Classification of Proteins Chemistry Database (SCOP)
http://www.sigmaaldrich.com/chemistry.html
UniProt http://www.uniprot.org/
Quantum Chemistry
Glossary of Common Terms and Abbreviations in Quantum Chemistry (Karl K. Irikura)
http://cccbdb.nist.gov/glossary.asp
QCLDB II Quantum Chemistry Literature DataBase http://qcldb2.ims.ac.jp/
Reactions:
WebReactions http://webreactions.net/ Help Screen: http://webreactions.net/tutorial.html
Side Effect Resource (SIDER) http://sideeffects.embl.de/
Safety:
OSHA Occupational Chemical Database https://www.osha.gov/chemicaldata/
Solvents:
SOLV-DB (NCMS – National Center for Manufacturing Sciences) http://solvdb.ncms.org/
Spectral Data:
EUROSPEC, International Spectroscopic Database http://www.is-db.org/
Spectral Data for Organic Compounds (National Institute of Advanced Industrial Science and Technology
(AIST), Japan) http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng
Help Screen: http://riodb01.ibase.aist.go.jp/sdbs/LINKS/help_eng.html
Spectral Data (EPA) http://www.epa.gov/ttn/emc/ftir/data.html
MassBank: High Quality Mass Spectral Database (National Bioscience Database Center, Japan Science
and Technology Agency) http://www.massbank.jp/ Help Screen: How to use Mass++ on left
ribbon
RRuff http://rruff.info/
Spectral Database for Organic Compounds, SDBS (National Institute of Advanced Industrial Science and
Technology (AIST), Japan) http://riodb.ibase.aist.go.jp/riohomee.html (click English in left
ribbon)
Structures:
ChemSpider Structure Search http://www.chemspider.com/StructureSearch.aspx
PubChem Structure Search https://pubchem.ncbi.nlm.nih.gov/search/search.cgi
Theoretical Chemistry:
Theorectical Chemistry http://www.internetchemistry.com/chemistry/theoretical-chemistry.htm
Therapeutics:
US National Cancer Institute Developmental Therapeutics Program http://dtp.nci.nih.gov/index.html
Thermodynamics/Thermophysical/Physical Properties:
Data & Property Calculation Web Sites (University of Illinois, Chicago Thermodynamics Research
Laboratory) http://tigger.uic.edu/~mansoori/Thermodynamic.Data.and.Property_html A Portal.
Infotherm Thermophysical Properties Database (London)
http://www.rsc.org/Library/LICMember/Resources/Infotherm.asp
Joint Expert Speciation System, JESS (Tool for tool for thermodynamic and kinetic modeling of chemical
speciation in complex aqueous environments) http://jess.murdoch.edu.au/jess_home.htm
Physical Properties Database (PHYSPROP) http://www.srcinc.com/what-we-do/product.aspx?id=133
Tools:
GenamicsSoftwareSeek http://genamics.com/software/ It “…is a respository and database of [over 1300] freely-distributable and commercial tools for use in molecular biology and biochemistry.” Portal
MyGrid http://www.mygrid.org.uk/ “… suite of tools designed to ‘help e-Scientists’ get on with science
and get on with scientists”.
TeraGrid Bioportal http://www.renci.org/focus-areas/project-archive/bioportal
Toxicology:
ECOTOX (US Environmental Protection Agency) http://cfpub.epa.gov/ecotox/
Environmental Health and Toxicology Database (National Library of Medicine)
http://sis.nlm.nih.gov/enviro.html Its “Guide to choosing the right environmental health and
toxicology resource” http://sis.nlm.nih.gov/enviro/decisionguide.html A Portal.
EXTOXNET, the Extension Toxicology Network (University of California-Davis, Oregon State University,
Michigan State University, Cornell University, and the University of Idaho.)
http://extoxnet.orst.edu/ghindex.html
National Toxicology Program (US Department of Health and Human Services)
http://ntp-server.niehs.nih.gov/
Toxicology directories (DMOZ) http://www.dmoz.org/Science/Biology/Toxicology/ A Portal.
Miscellany:
CSAR: Community Structure-Activity Resource http://csardock.org/
FDA Unique Ingredient Identifier http://fdasis.nlm.nih.gov/srs/srs.jsp
Kinase Knowledgebase http://www.eidogen.com/kinasekb.php
MatWeb: Material Property Data http://www.matweb.com/index.aspx
OCHEM Database: Online Chemical Modeling Environment project http://ochem.eu/
Integrated Spectral Data Base System for Organic Compounds
http://sdbs.db.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng
Chemical & Physical Property Information Resources
https://en.wikibooks.org/wiki/Chemical_Information_Sources/Physical_Property_Searches
From:
Murl M. Winters
Associate Library Director
Kendrick Library