24 Questions 72 Answers 0 Followers
Questions related from Khawar Sohail Siddiqui
I want to convert a SMILES code into a 3D SDF and PDB files to use for docking.I am using the following module: http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html The...
02 February 2019 7,553 5 View
I am looking for a free web based docking tool that takes into account backbone protein flexibility via induced-fit upon ligand docking?
02 February 2019 7,521 8 View
I am looking for kcat values (glucose and ATP) of hexokinase enzyme from common bakers yeast under physiological conditions (~pH 8, ~ 25 Deg C) along with reference preferably using...
07 July 2018 8,349 4 View
I need the exact diameter of ortho silicic acid, Si(OH)4. Kindly provide reference if possible. Thanking in advance for help.
05 May 2018 3,572 5 View
Although HRP lives under darkness most of its natural life, what possible biological role Energy transfer from Trp to heme can have? Can it possibly effect Fe reactivity in Compound I or II if...
06 June 2015 4,776 3 View
I want to determine which amino acids in a Protein structure are involved in Hydrophobic core. Is there a simple tool which requires a PDB file as input?
10 October 2014 1,180 5 View
If it is realized that the open-access journal you submitted your manuscript has a bad reputation, how best to proceed? The manuscript has not even been send to reviewers as yet. The Editor does...
08 August 2014 9,958 2 View
I want to construct a calcium standard curve using Calcium-Green dye and my own 1-39 uM calcium chloride solution. Is it possible to construct a good standard curve without using the commercial...
09 September 2013 3,082 3 View
I want to completely hydrolyze a peroxidase enzyme with NITRIC ACID to determine Calcium content by ICP. Can anybody tell me a tried and tested simple recipe for complete protein hydrolysis...
08 August 2013 7,694 5 View
The protein has 3 Tyr and 3 Phe and 0 Trp residues. It show a sharp peak at 365 nm corresponding to Phe and 3 peaks between 272 and 285 nm corresponding to Tyr but I am wondering what a positive...
05 May 2013 5,993 3 View
Is it possible that unfolding of a heme protein followed by trp fluorescence show decrease in intensity at 336 nm with increasing temperature. Normally, in heme proteins, emission intensity...
03 March 2013 871 0 View
My calcium EDTA binding experiments at pH 4.5 and 5.5 using iTC200 in 20 mM sodium acetate are endothermic. The Ca-EDTA kit provided by Microcal gives exothermic peaks in 20 mM MES buffer, pH 5.7....
12 December 2012 5,758 9 View
I am doing calcium EDTA binding Exp using iTC at low pH 3-5. I am getting n values between 0.1 to 0.5. Any ideas what is the physical significance of fractional n values?
11 November 2012 9,164 2 View
At pH 3.5 to pH 4.5 which is the better and efficient reducing agent to break all 4 disulfide bonds in my peroxidase enzyme? Also which reducing agent and concentration is compatible with far-UV...
10 October 2012 2,864 11 View
Want to determine metals in some proteins by ICP. Will be grateful if somebody gives exact recipe for Sample preparation including hydrolysis acid, time, temperature and starting protein amount...
10 October 2012 9,168 1 View
I need to follow the release of Heme moiety from peroxidases by Fluorescent method. Is there any fluorescent method available (Intrinsic or extrinsic)? I do not presently have access to CD to...
09 September 2012 2,461 1 View
I want to detect calcium release from my protein in pH 4.5 aqueous buffer by dyes such as Calcium green, but I am not sure whether these will work at pH 4.5 and will it be soluble? Does anyone...
09 September 2012 6,949 3 View
Got endotherm of protein only and protein+ ligand. Can any body point to the right Equation to use to determine binding constant from DSC unfolding curves?
09 September 2012 7,169 7 View
I have generated biphasic kinetic data. The first phase (low substrate/low v) data ia easy to plot using Michaelis-Menten plot using enzyme kinetics (EK2) module linked to Sigma-plot. Can anybody...
08 August 2012 6,245 20 View
As a general rule if any exothermic biochemical reaction has a certain enthalpy at 25 degree C,will the enthalpy decrease or increase at 50 degree C?
08 August 2012 2,358 3 View
We have extracted minute amounts of proteins with SDS and now want to precipitate the proteins for analysis. We already tried cold acetone, TCA etc but nothing worked. Any ideas are welcome. Thanks
07 July 2012 540 5 View
When I treat Humic acid with ligninase enzymes, its absorbance at 280 increases. Most references say that absorbance should decrease. What may be the reason?
07 July 2012 1,578 8 View
I want to run polystyrenesulfonate markers on size-exclusion column but my AKTA is only fitted with 280 nm UV-detector. Does PSS absorb at 280 nm? In the literature refractive index (RI) detector...
07 July 2012 190 0 View
I have a set of ~40-50 protein sequences. I want to find motifs like MEME tool but most importantly, I want a tool that can extract a consensus sequence like a scanprosite pattern e.g....
01 January 1970 2,874 6 View
