If a PDB coordinate file has missing residues. How can i repair the protein?

More Malathi Kullappan's questions See All

In beta-lactamases..ex: OXA-23, KPC-3 ..etc., the number after the enzyme indicates what?

beta lactamases...the numbers OXA-23, OXA-143, KPC-2, IMP-1 what these numbers are denoting?.

06 July 2017 6,755 2 View

How to run MD simulation for metallo enzymes having zn in GROMACS?

I want to do MD simulation for metallo enzyme as well as protein-ligand complex in GROMACS. But when i use the pdb structure with zn ions it showing error. Help me to sort out this problem. Which...

10 November 2016 4,488 4 View

How can I rectify the following error in Gromacs?

In grompp in ion.trp filr creation there occur error. Fatal Error, Too much Warning (1), use option -maxwarn. could anybody tell me how to use this option, if i use this option its asking for...

02 March 2015 9,217 3 View

In GROMACS when I give a PDB file its showing the error that HE1 atom not found in topology. How can I rectify it?

gromacs forcefield error

02 March 2015 7,032 2 View

Can anybody send gromacs tutorial for protein - ligand complex MD simulation in ubuntu?

gromacs tutorial for simulation

02 March 2015 3,737 0 View

How can I rectify the following GROMACS error? Fatal error: Atom HB3 in residue SER 3 was not found in rtp entry SER with 8 atoms while sorting atoms.

rectify my error Fatal error:Atom HB3 in residue SER 3 was not found in rtp entry SER with 8 atomswhile sorting atoms.

02 March 2015 1,600 10 View

How can I get a protein-ligand complex from sybyl x 2.0 for MD run and how can we separate the ligand from the protein?

sybyl x protein - ligand complex

02 March 2015 210 2 View

Why are we adding hydrogen, removing side chains and removing ligand substructure in molecular docking?

I'm referring to molecular docking sybyl version 2.0

09 October 2014 8,334 5 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Do anyone here can help us in the field of molecular docking?

We have synthesized various metal complexes with different environment around the metals. Now to see the application of synthesized complexes we need this study also. we are also interested in...

01 March 2021 1,899 2 View

What's the concentration recommend for recombinant protein use in western blotting?

I'm currently working having problem with the concentration for recombinant protein use in western blot, the one been used is Recombinant Human CD19 Fc Chimera Protein-rndsystem which does not...

24 February 2021 8,514 3 View

What program can I use to caclulate dipole moment efficiently and without the need of excessive computation?

Hi, I am a third year chemistry undergrad doing my group project in which I need to predict the HPLC retention time of 20 aromatic molecules. to do this we require the chemical properties of these...

24 February 2021 1,384 3 View

Will SARS-CoV-2 Spike be broken into S1 and S2 by denaturing conditions?

Hello, I am performing a western blot of my SARS-CoV-2 Spike-pseudotyped lentiviral particles. I denature my virus by adding concentrated virus to 2X Laemmli buffer at 1:1, then boiling for...

17 February 2021 4,844 4 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

Can I use asymmetric PCR amplification on a pool of circular plasmids to increase each plasmid's signal?

Hello, Here is my experiment: I transfect in a plasmid that has been cut once (a linear piece of dsDNA) into human cultured cells. I wait 48hrs to allow the cells to "repair" the plasmid making...

10 February 2021 6,090 3 View

Ligands with 3,4,5-trihydroxyphenyl group?

Hi In the design of a bidentate ligand with imine group, is it okay to have a 3,4,5-trihydroxyphenyl group in the structure? In other words, does the 3,4,5-trihydroxyphenyl group compete with...

08 February 2021 4,977 7 View

Is it possible to quantify recombinant protein in the supernatant using SDS PAGE ?

I would like to quantify a recombinant protein (with native signal sequence) secreted by Pichia pastoris using the SDS PAGE. Since my standard protein (plant origin) is not pure, I would like to...

07 February 2021 3,880 9 View

Filippo Prischi

Hello,

It very much depends on the structure and on the reason why you need a complete structure. If it is a short loop, you can easily model it by hand using tools like Swiss-PDB viewer. If it is a larger part of your protein (roughtly >10/15 residues) you can try to do homology modelling (if you have the structure of an homologue protein) or something a bit more adventurous like denovo modelling.

Jacob Schwartz

Filippo's answer is the way everyone I know does this.