Category:Cheminformatics: Difference between revisions

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Chemical Informatics is the art and science of manipulating chemical structure, particularly in a biological context. Many but not all of us are mainly looking for new ligands for biological targets.
Chemical Informatics is the art and science of manipulating chemical structure, particularly in a biological context. Many but not all of us are mainly looking for new ligands for biological targets, or trying to predict the function of proteins by the ligands they recognize. Our contribution in this area includes [[SEA]], with [[ZINC]] in a supporting role.
 


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* [http://redpoll.pharmacy.alberta.ca/drugbank/ DrugBank] The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4300 drug entries including >1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and >3,000 experimental drugs. Additionally, more than 6,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Please cite: Wishart DS et al., DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 1;34
* [http://redpoll.pharmacy.alberta.ca/drugbank/ DrugBank] The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4300 drug entries including >1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and >3,000 experimental drugs. Additionally, more than 6,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Please cite: Wishart DS et al., DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 1;34


== Freeware ==
== Free cheminformatics software ==
Most completely free software for chemical informatics is part of the [http://www.blueobelisk.com Blue Obelisk Movement]. We note some of these, as well as other packages, below:
[[:Category:Free | Free software]]
* [http://jmol.sourceforge.net JMol] - so good, Nature picked it.
* [http://cdk.sourceforge.net CDK] - many of these packages, such as Bioclipse, make use of CDK.
* [http://openbabel.sourceforge.net OpenBabel]/[http://joelib.sourceforge.net/ JOELib] - format conversion
* [http://www.bioclipse.net Bioclipse] - a visual platform for chemical and bio-informatics.
* [http://www.knime.org Knime] - a free Scitegic PipelinePilot style program
* [http://www.mayachemtools.org MayaChemTools] - a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs


== Freely Available Databases ==  
== Freely Available Databases ==  
* [[ZINC Database]]
[[:Category:Free | free databases]]
* [[PubChem]]
** [http://www.ncbi.nlm.nih.gov/Class/PubChem/course.html Principles of PubChem NCBI Training Course]
** [http://www.indiana.edu/~cheminfo/PubChemHandout.doc PubChem Handout Word document (Dana Roth, Caltech) ]
 
* [[KEGG]]
* [http://cdb.ics.uci.edu/CHEM/Web/ ChemDB @ UCI] - public database of small molecules and related chemical informatics resources
* [http://bioinf.charite.de/superdrug/ SuperDrug] - a conformational drug database
* [http://bioinformatics.charite.de/supernatural/ SuperNatural] - searchable database of available natural compounds
* [http://bioinformatics.charite.de/superligands/ SuperLigands] - a PDB ligand database
* [http://cheminf.cmbi.ru.nl/biometa/ BioMeta ] - a database of metabolites derived from KEGG
* [http://xpdb.nist.gov/chemblast/pdb.pl ChemBlast] - a tool to find the same ligand in many PDB structures
 
== Free information ==
* [http://ccl.net/cca/documents/MMCC_Results/ MMCC Results Newsletter]
* [http://en.wikipedia.org/wiki/Computational_chemistry Chemical Informatics @ Wikipedia]]
* [http://ccl.net Computational Chemistry List]
* [http://www.redbrick.dcu.ie/~noel/linux4chemistry/ Linux for Chemistry]
* [http://pubs3.acs.org/acs/journals/supporting_information.page?in_manuscript=ci049884m Caco-2 permeability]
* [http://www.cheminformatics.org/datasets/li/bbp2.smi Blood-brain-barrier penetration set]
* [http://cheminfo.informatics.indiana.edu/cicc/cis/index.php/Main_Page Chemical Information Wiki]
 


== Free datasets ==
[[:Category:Free | free datasets ]]


== Free to Academics engaged in non-commercial projects, etc. ==
== Free to Academics engaged in non-commercial projects, etc. ==
* [http://www.chemaxon.com ChemAxon JChem Marvin]
[[:Category:Freecom | Free or cheap to academics, costs to companies (freecom)]]
* [http://www.eyesopen.com OpenEye]
* [http://www.xemistry.com Cactvs]
* [http://www.cgl.ucsf.edu Chimera]
* [http://pymol.sourceforge.net PyMol]
*


== Useful Sites ==
== Useful Sites ==
* [http://bioinfo-pharma.u-strasbg.fr/template/jd/index.php Rognan/Strasbourg]
[[Useful Websites]]
* Jain
* [http://www.chembiogrid.org/cheminfo/smi23d/ smi23d - 3D Coordinate Generation]
* [http://cactus.nci.nih.gov/services/translate/ Online SMILES Translator and Structure File Generator]
* [http://www.chemaxon.com/marvin/doc/user/molconvert.html Molecule file conversion with MolConverter]
* [http://www.ccl.net/ Search the CCL for others]


== Feeware ==
== Feeware ==
* [http://www.molecularnetworks.com Molecular Networks]
[[:Category:Commercial | Commercial software]].
* [http://www.molinspiration.com Molinspiration]
* [http://www.schrodinger.com Schrodinger]
* [http://www.pipelinepilot.com Pipeline Pilot]
* [http://www.biosolveit.com BioSolveIT]
* [http://www.daylight.com Daylight]
 


== Database Vendors ==
== Database Vendors ==
* MDL
[[:Category:Commercial | Commercial database vendors]].
* Beilstein
*
 


== Applications ==
== Applications ==
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== Journals ==
== Journals ==
* [http://pubs3.acs.org/acs/journals/toc.page?incoden=jcisd8 JCIM]
[[Journals]]
* [http://springerlink.metapress.com/content/1573-4951/ JCAMD]
* [http://pubs3.acs.org/acs/journals/toc.page?incoden=jmcmar J Med Chem]
* [http://pubs3.acs.org/acs/journals/toc.page?incoden=jacsat JACS]
* [http://www.pnas.org/ PNAS]
* [http://www.chemistrycentral.com/ CCJ Chemistry Central Journal]
* [http://www.biomedcentral.com/ BioMed Central]
* [http://www.biomedcentral.com/browse/bysubject/  Curr. Op. Drug Discov. Devel.]
* [http://www.elsevier.com/locate/issn/13675931 Curr. Op. Chem. Biol.]
* [http://www.nature.com/nature/ Nature]
* [http://www.sciencemag.com/ Science]
* [http://www.nature.com/nbt/ Nature Biotech.]
* [http://www.nature.com/drugdisc/ Nature Drug Discov.]
* [http://www.nature.com/nchembio/ Nature Chem. Biol.]


[[Category:Portal]]
[[Category:Topic]]
[[Category:Topic]]

Latest revision as of 17:06, 21 August 2014

Chemical Informatics is the art and science of manipulating chemical structure, particularly in a biological context. Many but not all of us are mainly looking for new ligands for biological targets, or trying to predict the function of proteins by the ligands they recognize. Our contribution in this area includes SEA, with ZINC in a supporting role.


Blogs and Communities

Data and directory services

  • DrugBank The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4300 drug entries including >1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and >3,000 experimental drugs. Additionally, more than 6,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Please cite: Wishart DS et al., DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 1;34

Free cheminformatics software

Free software

Freely Available Databases

free databases

Free datasets

free datasets

Free to Academics engaged in non-commercial projects, etc.

Free or cheap to academics, costs to companies (freecom)

Useful Sites

Useful Websites

Feeware

Commercial software.

Database Vendors

Commercial database vendors.

Applications

Docking Programs

There is a dedicated page for Available Docking Programs.

De Novo Design

- One

Database Management Systems

- Daylight - MDL - Oracle - MySQL

Desktop modeling

- PyMol - Chimera

  • Comprehensive Packages ( Accelrys, Sybyl, etc)
  • ADME(T)
  • QSAR
  • Bioisosteres
  • hit-to-lead

US Government Grants

  • P20 ECCR
  • NIH Roadmap


Journals

Journals

Subcategories

This category has the following 2 subcategories, out of 2 total.

R

S

  • SEA(1 C, 8 P)