Can anybody suggest a free web-based induced-fit docking tool?

I am looking for a free web based docking tool that takes into account backbone protein flexibility via induced-fit upon ligand docking?

01 February 2019 7,439 8 View

How to save/export a 3D SDF file using Open Babel?

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...

01 February 2019 7,418 5 View

What are dimensions of ortho-silicic acid?

I need the exact diameter of ortho silicic acid, Si(OH)4. Kindly provide reference if possible. Thanking in advance for help.

04 May 2018 3,480 5 View

Is there any biological role (significance) of FRET from Trp residues to heme in peroxidases such as in Horseradish peroxidase?

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...

05 June 2015 4,665 3 View

Is there a bioinformatic tool to determine hydrphobic core amino acids by inputing a PDB file?

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?

09 October 2014 1,098 5 View

What to do if you realize after submission to an open-access journal that it has bad reputation?

07 August 2014 9,881 2 View

How can I construct a Calcium-Green Standard curve without using commercial kit?

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...

08 September 2013 3,001 3 View

What is the recipe for complete protein hydrolysis using nitric acid?

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...

07 August 2013 7,619 5 View

What is a positive peak at 305 nm in a purified protein using Near-UV CD show?

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...

04 May 2013 5,905 3 View

Trp to heme energy transfer.

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...

02 March 2013 805 0 View

How to calculate the fraction metabolized of a drug by an enzyme using clearance(ml/min) values of the metabolite formed?

I am trying to find the fraction metabolized of a drug by CYP and UGT enzymes. I am unable to get the values of fraction metabolized (Fm) directly from the literature. Can we calculate the Fm of a...

21 February 2021 5,379 2 View

How to avoid ATP degradation while performing ATP assay?

I am using the ATP Assay Kit (Colorimetric/Fluorometric) (ab83355) for measuring intracellular ATP from treated cell lines. Although my standards are wokring fine when using the fluorometric...

15 February 2021 3,746 4 View

How long does it take to design and validate transition state analogue inhibitors?

Hi, I'm asking from the point of view of designing a research plan: How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope...

14 February 2021 2,610 1 View

Kinetics of Enzyme production in Recombinant E Coli?

Hello, I am trying to find kinetic information (such as rate of enzyme production etc.) on the expression of taq polymerase in E-Coli after inserting a recombinant plasmid. Any help would be...

12 February 2021 1,386 3 View

Any probe or assay for the detection of Cysteine in yeast invivo ?

Dear fellow researchers, I would like to detect the cysteine levels for yeast in vivo. I would really appreciate if anyone could suggest me any fluorescent probe or assay kit available. Currently...

11 February 2021 3,292 3 View

No title

Hello! I want to determine the activity of my in house Reverse Transcriptase enzyme. For this, I have used Thermo's Enzcheck Reverse Transcriptase assay kit. I used commercial Thermo RT enzyme to...

08 February 2021 7,285 1 View

How define one baker unit(BU) is the amount of hydrogen peroxide catalase ?

07 February 2021 2,006 1 View

Which fungicide are good for primary cells? Does it yeast contamination? How to get rid of them without killing the cells? How to get rid of spores?

Hello! Our lab is working with primary cells which we are isolating from the colorectal tissue. During the isolation, we are washing the tissue with pen-strep and then also add some pen-strep in...

07 February 2021 8,258 3 View

Does DNA A-tailing survive after agarose gel electrophoresis and purification?

Hi everyone, I need to clone in pGEM-T vector the result of amplifying a metagenomic library by PCR with a high fidelity polymerase but I only want to clone the fragments of an specific size...

04 February 2021 6,051 8 View

How to Remove DNA From a Sample Without Rupturing Yeast?

I transformed a plasmid into yeast and selected for transformants by growing them in a selective media (liquid, not agar plate). My experiment requires that I continually grow/ split these...

01 February 2021 9,936 2 View