Can someone suggest free online/offline tool to predict the drugliness of the multiple small compounds in sdf format? I tried DrugLito, but it is predicting incorrect values. So I am looking for an alternative.
I would like to do classical MDS of a protein containing phosphorylated cysteine (3-oxoalanine) using GROMACS. Which force field should I use?
07 August 2019 7,495 4 View
I have performed simulation using gromacs. The protein is of two chains, I am trying to understand the changes in mmpbsa values between the two chains but I get following. What could be possible...
02 March 2019 2,121 3 View
I have performed a protein-protein simulation. I wish to see the change in binding between protein chain A & chain B. How to create a index files of chain A & B and do the analysis? Like GROUP 1 :...
02 March 2019 6,435 4 View
I wish to study the change in interaction of the small molecule with the protein in respective to change in pH. GROMACS focuses most on protonation state and not directly on pH. So how can I...
01 February 2019 3,264 5 View
We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...
03 April 2018 4,171 0 View
02 March 2018 7,266 1 View
I have gone through the paper entitled "Quantifying the chemical beauty of drugs by Bickerton et al., 2012" but I am unable to understand the normal values for each parameter (MW, LogP, etc.)...
05 June 2017 7,915 0 View
When there is a set of parameters for drug-likeness such as MW, LogP, HBD, HBA, etc., why are some commercially available drugs which are known to best don't satisfy it?
05 June 2017 2,333 5 View
When I go with Gromacs protein simulations, should I consider about performing long run (at least 100ns) or multiple runs (at least 2 runs)? Which one of these could be more reliable and why?
03 April 2017 2,799 3 View
I used mindist of gromacs to find the distance between the proteins (native and mutants) and the metal (metalloprotein) over the simulation period. I have the output in form of graphs. Is there a...
02 March 2017 680 2 View
"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....
10 August 2024 8,621 1 View
Hello experts, Does anyone know any free software about retention index prediction ?
08 August 2024 7,403 2 View
I have an antibody binding generic protein and I need to compare its activity in a free and immobolized form. I understand that there are a number of methods to determine Kd value of a free...
05 August 2024 5,311 0 View
for eg. transition shock scale
01 August 2024 5,998 0 View
Because I have realized that the world tends more and more to do open and free science and there is a trend more and more to choose free databases, free tools and open access platforms.
01 August 2024 10,046 1 View
I want to do 2,3-butanediol dehydrogenase(BDH) enzyme purification to confirm its activity for 2,3-butanediol. Before that, I need to confirm which N or C terminal tagging is better for enzyme...
28 July 2024 366 3 View
I am currently performing cell-free DNA (cfDNA) extraction from plasma using an in-house developed kit that employs silica-coated magnetic beads. My protocol works effectively with plasma obtained...
28 July 2024 3,559 0 View
Do you know of any online international conferences that offer free discussions? I am looking for examples in the field of molecular ecology and DIY biology.
28 July 2024 6,501 0 View
I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...
19 July 2024 4,120 5 View
I would like to use biofilmQ to analyse confocal laser image, how can do?
16 July 2024 7,628 2 View