Is the any software for finding upstream and downstream sequence of a gene?

For cloning purpose when we design primers, we need to deal with the upstream and downstream sequence of the cDNA. could you please suggest a software which would be appropriate in doing that?

06 July 2016 9,275 7 View

How we could calculate the range of phi and psi angle between a monopeptide.

For example, attached file is representing a .pdb file containing a peptide between two glycine. How we could measure the range of phi and psi angles here. Thanks in advance for your help and...

01 February 2016 3,067 4 View

Can anyone suggest a program to read trajectory files of different formats?

Can anyone suggest a program which could read all the different trajectory files (eg., .xtc, .dcd, .mdcrd) coming from different MD Simulation program packages.

01 February 2016 7,995 4 View

Which one of the following would be a suitable method to calculate the binding affinity/binding free energy of a protein ligand interaction?

02 March 2015 5,875 1 View

How to model a protein with multiple domains and no template covering more than one domain?

I'm trying to model a protein which has multiple domains and templates available covering small parts of the sequence. It is a 4500 aa protein and to moderately covering the sequence it needs 7...

11 December 2013 2,860 19 View

Double Conformation of amino acid residues in a PDB file while runing MD Simulation

I'm preparing a PDB to run a MD simulation in AMBER. I have noticed that some of the amino acid residues exist in double confirmation. Should I remove all the double confirmation before the...

06 July 2013 1,819 3 View

Can someone recommend a good theoretical method by which two mutant variants could be differentiated?

Stability of protein mutants: I'm trying to design thermostable variants of a protein. Is it possible to theoretically differentiate them without doing simulation? What would be the parameters I...

06 July 2013 4,758 5 View

How to relate loop flexibility with enzyme catalysis?

I'm working with an enzyme where some of the loops are playing important roles in catalysis. How could I study the relation of loop flexibility with the re-activity (computationally)?

05 June 2013 3,213 6 View

Can anyone help me with a suitable method for computational study of the thermal stability of protein mutants?

I'm studying stability of certain enzymes with their mesophilic and thermophilic homologues using MD Simulation methods. Using the information obtained from the study I'm trying to design point...

05 June 2013 2,959 3 View

I need help with my MMPBSA calculation

I am running a binding energy calculation (MM-PBSA) for protein-ligand complex using Amber11 and AmberTools 1.5. I am following a Ross Walker tutorial (Link:...

01 February 2013 3,412 0 View

Chlorinated organic formation in odor control scrubbers using hypochlorite?

I'm involved in a study of odor control technologies for municipal wastewater treatment plant. One of the control options involves a chemical 2-stage (acid/alkaline) packed bed scrubber. The...

03 March 2021 3,661 2 View

What techniques can I use to determine the miscibility of polymer blends?

The term miscibility refers to the single-phase state in thermodynamics. I do not mean the compatibility of different components. To determine the miscibility I know several techniques such as...

03 March 2021 4,107 4 View

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 2 View

Ester cleavage conditions?

Hi all, I need to cleave the ester in Ethyl 2-amino-1H-imidazole-5-carboxylate to make the carboxylic acid and retrieve the product from solution to use in downstream applications of linking to...

01 March 2021 8,766 3 View

Shall I skip the measurement model in SmartPLS?

Hello everyone, I had run a mediation model in SmartPLS using questionnaires that were already validated among my statistical population. A professor who edited my paper -though she is not...

01 March 2021 3,052 3 View

What is involved in morphological changes of SEM images of a substance?

In the sem analysis of CaCO3 nanaoparticles, the morphology images showed spherical shaped particles but the proposed morphology for these type of nanoparticles is trigonal. I prepared the...

01 March 2021 1,960 4 View

I have designed reflectarray element and feeding it though Horn Antenna on HFSS. After full wave simulation, I am not getting desired results?

I have designed reflectarray element to generate OAM beams at 5.8GHz and feeding it though Horn Antenna on HFSS. After full wave simulation, i am not getting desired results i.e Radiation pattern...

01 March 2021 9,701 5 View

How to address this issue in the analysis of Real-Time PCR results?

To dear Researchers, I was analyzing a series of concentration for estimation of Real-Time PCR efficiency. The concentration was 1:10. I used MS-excel to evaluate Slope. The result of slope was -8...

01 March 2021 8,683 4 View

Can I download BibExcel for MacOs?

Hi everyone, I would like to ask how I can download BibExcel software for MacOs? There are some links which are supported by Windows but I could not find it for Mac. or is there any other software...

01 March 2021 652 1 View

How to remove DCU and HOBT from my reaction?

I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??

28 February 2021 2,153 1 View