Med chem stuff
Some links to useful things (under construction -if you use something post a link. Ta)
The ACS Daddy - http://www.acsmedchem.org/ddlinks.html
Al’s Notebook - http://www.alsnotebook.com (experimental procedures for commonly performed reactions)
ClusterMed - http://demos.vivisimo.com/clustermed (really nice PubMed clustering search engine, helps narrow down those overwhelming PubMed results)
iHOP - http://www.ihop-net.org/UniPub/iHOP/ (Database with info on genes/proteins)
ChemExper - http://www.chemexper.com/ (online chemical supplier catalogue searching)
Marvin - http://www.chemaxon.com/demosite/marvin/index.html (online LogD, LogP, PSA, Lipinski-type stuff. Very nice interface. Not sure if you should use it with proprietary compounds though)
Goodman Group - http://www.ch.cam.ac.uk/magnus/ (chemical calculations in Java)
Scitegic (Pipeline Pilot) http://www.scitegic.com/
ACD Labs - http://www.acdlabs.com/ (useful NMR software, as well as Structure Design Suite)
Relibase - http://relibase.ccdc.cam.ac.uk/reli-cgi/rll?/reli-cgi/general_layout.pl?home (ligand overlays and binding mode comparisons)
Pawson Lab - http://pawsonlab.mshri.on.ca/index.php?option=com_content&task=view&id=30&Itemid=63 (protein domain information)
Protein Data Bank - http://www.rcsb.org/pdb/home/home.do (X-ray/NMR structures)
Expasy - http://www.expasy.org/ (proteomics + protein knowledgebase)
WIPO - http://www.wipo.int/pctdb/en/ (patent searching (not by chemical structure))
Pubmed - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed (biomedical literature searching)
Chemical Computing Group - http://www.chemcomp.com/ (commercial software provider)
Known toxicophores - http://www.ics-ir.org/jics/vol2/n4/articles/jicsv2n4r1.pdf (pdf from Journal of the Iranian Chemical Society)
pKa data - http://daecr1.harvard.edu/pKa/pKa.html
pKa data II - http://www.chem.wisc.edu/areas/reich/pkatable/index.htm
Drug information - http://www.mdli.com/products/knowledge/drug_data_report/index.jsp (MDL)
Drug information - http://www.iddb.com (Investigational Drugs Database)
If we are listing tools for medchem here then I’d like to offer an alternative to the heavily molecular modelling
CCG software which is really for teh use of computational experts. There are many software companies now
offering tools specifically designed for medicinal chemists. ACD/Labs (www.acdlabs.com) is one of them.
Their lead optimisation sofwtare ACD/Structure Design Suite can help to specifically optimise a structure
for its physical properties.
Comment by Sanji Bhal — February 13, 2007 @ 3:38 pm
I don’t think the ACDlabs software is an alternative to CCG, they are completely different. (sorry I can’t read all the comment).
One of the attractive features of the CCG software is that you can write “skins” that can be designed for a particular type of user.
Comment by Chris — February 15, 2007 @ 4:04 pm
I have never used the ACD Labs structure design suite, so don’t feel capable of commenting on what it does, and how well
(although I currently used the ACD NMR software and it does the job nicely). I have used MOE (CCG) and liked it a lot, even
as a non-expert I found it fairly simple to use (unlike the Tripos suite), especially some of the nifty Gizmoes that you can add
in to visualise contacts in the active site with one click. Undoubtedly for your Average Joe bench med chemist MOE and
Sybyl are total overkill.
I was however never anything more than a comp chem tinkerer, so there are no doubt many layers of functionality within
all these packages that suit some researchers and not others, and things that some packages do a lot better than others
(as I remember it the MOE docking algorithms were rather unreliable, but this was about 3 years ago). And, of course,
MOE and Sybyl are horrendously expensive.
Comment by totallymedicinal — February 15, 2007 @ 8:14 pm
[...] New stuff Filed under: Uncategorized — totallymedicinal @ 10:47 am I have cleaned up some of the blogroll, where some blogs have atrophied or disappeared. I have also added a couple of links to the useful med chem stuff [...]
Pingback by New stuff « TotallyMedicinal — May 12, 2007 @ 10:47 am
You may want to check out the Peptide Resource Page, they have lists of companies that sell custom peptides, peptide synthesizers, etc… but of greater interest to medicinal/synthetic chemists is their list of peptide synthesis reagents. There is a pretty big section of companies that sell un-natural amino acids, coupling reagents, etc… Just thought this group might be interested.
-John (med chemist austere)
Comment by john — July 31, 2007 @ 4:31 am
You may want to check out the Peptide Resource Page, they have lists of companies that sell custom peptides, peptide synthesizers, etc… but of greater interest to medicinal/synthetic chemists is their list of peptide synthesis reagents. There is a pretty big section of companies that sell un-natural amino acids, coupling reagents, etc… Just thought this group might be interested.
Sorry I forgot the URL in the last post. See:
http://www.peptideresource.com/
http://www.peptideresource.com/peptide-synthesis.html
-John (med chemist austere)
Comment by john — July 31, 2007 @ 4:33 am
I added a section called Drug Discovery Resources to my site all comments/suggestions/additions welcome. Still very much a work in progress.
Comment by Chris — August 24, 2007 @ 9:32 am
very interesting, but I don’t agree with you
Idetrorce
Comment by Idetrorce — December 15, 2007 @ 1:50 pm
One of the things I’m often asked for by small companies of academic groups who are looking to bring a compound forward is list of assays/properties they should evaluate.
After searching around I can’t find such guidance in the public domain so I’ve tried to put together a checklist that I hope will be useful.
http://homepage.mac.com/swain/Sites/CMC/DDResources/preclinical_checklist.html
Chris
Comment by Chris — June 1, 2008 @ 8:16 am
Thanks Chris, that is very useful
Comment by TotallyMedicinal — June 1, 2008 @ 1:42 pm