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Questions related from Muhd Hanis Md Idris
I had run homology modelling on unknown protein structure using I-Tasser and Robetta. Both are consensus that the mutation on the protein is at the loop part of the protein. However, the structure...
09 April 2023 8,388 1 View
I had construct the protein model using three software, I-TASSER, Raptor-X and Swissmodel. But, none of them are fulfilled Ramachandran plot criteria. So, how to improve the model for the next...
17 June 2022 645 4 View
I had predicted 3D structure of protein using I-TASSER as there are no template that satisfied match with the protein sequence. Then I checked the Ramachandran plot to determine the reliability of...
24 July 2019 6,911 2 View
I had ran molecular dynamic simulation on apo protein using TIP3P, TIP4P, TIP4PEW and SPC for 25 ns to establish the most suitable solvent model for specific protein. However, none of them gave...
25 May 2018 10,099 3 View
I had tried using indomethacin (10 mg/kg) and diclofenac (25 mg/kg) as control in cotton pellet induced granuloma study, but during the experiment, the rats were died because of ulceration. I use...
22 November 2017 5,789 0 View
I used RAW264.7 (2 x 106 cells in 100 ul) at below passage 12 and induced with LPS at concentration of 0.1, 10 and 100 ug/ml and incubate for 22 hours. I measure the nitric oxide level and found...
04 September 2016 2,237 4 View
How much the cells that I need to use for developing growth curve of the cells? What is the size of cell culture plate that I need to use? Is there any standard guideline to follow? At the moment,...
28 July 2016 2,649 4 View
I'm looking the free software as well as commercial software that can use to predict the side effects of the lead compound like liver toxicity and so on. Thanks.
28 April 2016 7,772 3 View
I want to determine the diversity of chemical compounds that I have collected by using principal component analysis (PCA). Which PCA software is suitable for me to use?
14 November 2015 1,177 40 View
There are many types of phosphodiesterase (PDE) as well as subfamilies of each type. What assay that we can do to identify the specific target of the drug using in vitro and in vivo study?
23 September 2015 4,169 3 View
I want to screen the compounds in Ligand Scout. So I need to convert the compound to lbd format as Ligand Scout only accept that format. Is it I need to do ligand preparation and generate...
10 August 2015 6,347 3 View
I had subculture RAW 264.7 cell but at passage 8, the morphology of the cells were change. Is it because of the macrophage is already activated? What the different between the normal and activated...
04 August 2015 5,005 17 View
I use Bouin's solution to fixed testis of rat. How long should I fixed the tissue using Bouin's solution? And then how can we process the tissue that is fixed using Bouin's solution? Is it...
15 June 2015 1,942 7 View
I already have a set of data for screening purposes. Do I need to develop decoy set from the data that I want to screen or I can use the other decoy database available? If I need to develop decoy...
23 April 2015 3,535 5 View
The pharmacophore is generated from structure and ligand-based drug design. How can we know the pharmacophore generated is valid for virtual screening? What the method can used?
18 April 2015 3,749 3 View
I want to evaluate the toxicity of the compound according to OECD guideline in order to determine the safety dose level. However, the compound is not enough for acute and subacute toxicity...
17 March 2015 7,252 3 View
I want to combine many PDB complex to generate shared pharmacophore. But the problem is when I generate shared pharmacophore of all PDB complex, I can't generate any shared pharmacophore. So what...
16 February 2015 8,082 6 View
May I know the different if we measure the cytokine level using ELISA and protein expression (Western blot and RT-PCR)? Some of the journal measure both.
06 February 2015 9,489 3 View
I plan to measure TNF-a, IL-1B, IL-6, IFN-gamma and MCP-3. Which method should I use? Which methods are convenience, reliable, easy and cost effective?
06 February 2015 2,583 10 View
I want to evaluate the reproductive toxicity of chemicals. Which guideline should I follow to test reproductive toxicity in vivo and in vitro?
19 December 2014 6,522 4 View
I need to build up a virtual library of the ligands for my in silico drug design. So I need guidance on how to build up the ligand library, the software to use and how to make sure the database...
20 November 2014 5,344 14 View
What the different between all the model? Preferably rat/mouse.
30 October 2014 8,702 8 View
