Latest Questions

Is it possible to do post-doc in a subject different from our PhD research topic?

Go to the profile of Irfan Pervaiz
Irfan Pervaiz on Dec 04, 2016 • 1 answer
The answer is a definite YES. There are two ways to look at the postdoc experien... Read more »
Go to the profile of Ramaswamy Narayanan
Ramaswamy Narayanan on Dec 08, 2016

What free docking programme would you recommend?

Go to the profile of Helen Turner
Helen Turner on Mar 01, 2016 • 5 answers
I would suggest that you start with Auto Dock4 first. Then you may want to try it with AutoDock Vi... Read more »
Go to the profile of Ramaswamy Narayanan
Ramaswamy Narayanan on Dec 11, 2016

RMSD issue...

Go to the profile of VIRENDRA NATH SRIVASTAV
VIRENDRA NATH SRIVASTAV on Feb 11, 2016 • 2 answers
As site editor for MedChemNet, I'm pleased to provide this response from networker Dr Harish Kundaikar: "The idea of simulation for 10ns seems to be just enough as this is the statistically significant amount of time basically needed to conclude anything from molecular dynamics. However being a medicinal chemist you would need much more simulation time in order to publish in reputed journa... Read more »
Go to the profile of Stella Bennett
Stella Bennett on May 31, 2016

Is there any article on effect of attachment of Omega Fatty acid to the active compound/molecule(s)/drug(s) for the betterment of drug metabolism.

Go to the profile of VIRENDRA NATH SRIVASTAV
VIRENDRA NATH SRIVASTAV on Jan 06, 2016 • 1 answer
You may want to take a look at the following references: PMCID: PMC3537895 doi:10.1016/j.molbiopara.2015.03.004 The question needed to be better defined. Then a simple Google query will give you possible answe... Read more »
Go to the profile of Ramaswamy Narayanan
Ramaswamy Narayanan on Jun 05, 2016

Can anyone post or mail me the link of video/ppt for briefing of GPR40/FFA1R Receptor mechanism (biology)

Go to the profile of VIRENDRA NATH SRIVASTAV
VIRENDRA NATH SRIVASTAV on Jan 06, 2016 • 2 answers
As site editor for MedChemNet, I'm pleased to post this response from networker Dr Harish Kundaikar: "If you wish to read about GPR40 class of receptors also referred to as Free Fatty Acid Receptors/Carboxylic Acid Receptor Family which includes GPR40 to 43 and GPR120; alongwith their Classification, Ligands, Biodistribution, and detailed Mechanisms including the possible role of oligomerisation in their functional regulation, refer to this article: “GPR40 Carboxylic Acid Receptor Family and Diabetes: A New Drug Target” V.... Read more »
Go to the profile of Stella Bennett
Stella Bennett on May 31, 2016

I go to poster images and do not see any images

Go to the profile of Simon Fricker
Simon Fricker on Nov 27, 2015 • 1 answer
Hello Simon, Thank you for getting in touch. Posters are not pre-uploaded into accounts, so unless you have used the ‘Browse’ option to upload them yourself there would not be any yet availab... Read more »
Go to the profile of Rosalind Hill
Rosalind Hill on Nov 30, 2015

Can anyone tell me about the 3D-QSAR. What is the actual meaning of 3D-QSAR. "Is inclusion of 3D-descriptors/properties or something related to spatial arrangement of the molecules"

Go to the profile of VIRENDRA NATH SRIVASTAV
VIRENDRA NATH SRIVASTAV on Aug 14, 2015 • 1 answer
3D-QSAR spans a broad range of methodologies, with the common thread being that all 3D-QSAR techniques involve at least one ligand property that can't be quantified without knowing a plausible 3D spatial conformation for the molecule. Some examples of 3D-QSAR include receptor-based QSAR (one takes into account explicit information about the ligand-receptor contacts), pharmacophore-based QSAR (from the ligand alone, one identifies the spatial relationship between potentially relevant pharmacophore features), shape-based QSAR (conformational information about the molecule can suggest propensity for binding to a given receptor), and finally physicochemical-based QSAR, in which activity is related to physicochemical properties that are best estimated through 3D structural assessment (e.g., amphiphilicity, polarizability, conformational stabilit... Read more »
Go to the profile of Gerald Lushington
Gerald Lushington on Aug 19, 2015

Is there any article published on "Mathematics behind Pharmacophoric features" I mean mathematical values different groups/functional groups- feature of pharmacophore (HBD, HBA, Aromatic ring, etc.)

Go to the profile of VIRENDRA NATH SRIVASTAV
VIRENDRA NATH SRIVASTAV on Aug 12, 2015 • 1 answer
Yes, the book by Todeschine and Consonni provides an exhaustive theoretical and practical assessment of virtually any molecular descriptor in common usage: http://onlinelibrary.wiley.com/book/10.1002/9783527613106 If you are focusing very narrowly on only those descriptors that are employed in pharmacophore characterization, then you may be able to hone in on an article that answers your question more immediately. I'm not certain of exactly what you mean by "mathematical values", but a comparison between the relative importance of specific pharmacophore features across different ligand classes is provided in the article by Zuccotto: http://pubs.acs.org/doi/abs/10.1021/ci034068k
Go to the profile of Gerald Lushington
Gerald Lushington on Aug 12, 2015

I am interested in knowing the lipinski parameters and TPSA/PSA for my molecules. Can anyone suggest me a reliable tool ( free downloadable version) for it?

Go to the profile of Sai Giridhar Sarma.K.
Sai Giridhar Sarma.K. on Jul 14, 2015 • 1 answer
There are a number of open source or other tools available to achieve your aim here. The RDKit API (http://www.rdkit.org/) allows you to calculate TPSA using the model published by Peter Ertl et ... Read more »
Go to the profile of Dr Nathan Brown
Dr Nathan Brown on Aug 11, 2015

A question for computational/medicinal chemists working in drug discovery: In your day-to-day work, which computational tools/programs (small or large; commercial or open source) do you find most useful? For which application(s)? Naming just one or two of your favorites would be much appreciated. Many thanks in advance!

Go to the profile of Jürgen Bajorath
Jürgen Bajorath on Jun 12, 2015 • 1 answer
It's always an interesting exercise to answer a question like this -- especially if one uses a fair number of different tools. After a bit of thought, I think I can narrow the list down to four programs that I find myself launching at least once (and often many times) in the course of most projects: 1) PyMol (http://sourceforge.net/projects/pymol/): in its earlier incarnations, the menu options were primitive and the command syntax was clunky, but this program has gotten increasingly friendly and I now count it as a great pal and confidan... Read more »
Go to the profile of Gerald Lushington
Gerald Lushington on Jun 17, 2015

Aside from PlosOne, which other good (impact factor) open access journals would you recommend for publishing research related to medicinal chemistry? Thank you very much for any feedback. Kind regards, Atanas -- http://homepage.univie.ac.at/atanas.atanasov/

Go to the profile of Atanas G. Atanasov
Atanas G. Atanasov on Jun 04, 2015 • 3 answers
Hi Atanas, I’d have to suggest Future Medicinal Chemistry’s sister publication Future Science OA, but I might be biased because I’m the editor! It’s a new launch, so is as-yet too young for an Impact Factor, but it’s content thus far is excellent quality, and is being very well read owing to the way we promote the conte... Read more »
Go to the profile of Future Science OA
Future Science OA on Jun 05, 2015