There are so many program that can do it like PyMOL, MMTSBToolset and FoldX (it optimizes pdb after mutation i.e. remove steric clashes)

Yes PyMOL dont do minimization but FoldX do it by using force field. If you have AMBER then you can use it for minimization after mutation.

Hi

you can try with Gaussview

I agree that with Schrodinger will be very easy. If I am not wrong you don't need of some package license, just download maestro (Maestro academic free campaign). However, I am not agree that you will need to optimize for so many iterations your protein because this will affects the whole X-ray structure, which is not good. Instead you can use Prime module of Schrodinger and/or restrict the minimization to some defined RMSD.

Indeed as was mentioned above, a lot of other packages can be used.

I usually use the Sirius software (free software form the university of San Diego supercomputer center, hhttp://www.ngbw.org/sirius/) to do the mutation. Once I am done with insilco mutation I usually minimize the structure using MD softwares with the proper force field, One can use the free MD software Gromacs which can also give you option to choice the force field you want to use (tutorial on minimization using gromacs can be found at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html)

VMD has something called "mutator", Extention > modelling > mutate residues. But basically it uses behind the scenes a program called psfgen, that usally uses CHARMM topology file to guess the position of the new inserted residue. I don't use it, since I directly use psfgen (I can put it my own scripts), but once I've tried it, and it is pretty simple to use and it works pretty well. The main issue was when I tried to mutate a "patched" residue, in CHARMM terminology. If you don't know what it means, than it is not something that might bother you. Before using it, you likely need a psf file (protein structure file) that can be produced with Extention > modelling > Automatic PSF builder if you don't like to spend to much effort on psfgen (read the manual and namd tutorials, it is pretty simple).

Wincoot and Chimera can be used

VMD is another good option

Vi

Hi. Most general purpose molecular modeling software allow you to mutate aminoacid residues and to post-refine the protein structure. I would recommend, for instances, Maestro from Schrodinger, Inc. However, if you want a free application that can do the job, you could use Swiss-PDBviewer, which has some interesting features, for a free application.

pymol. chimera, MOE, YASARA, Spdb etc

Hyperchem can do it. But I would go with xleap

PyMol

Use mutagensis option in PyMOL . It provides option for various rotamers of AA.

You can use PyMOL and MMTSB Toolset.

Coot is a good one too

Chimera can easily do this, it is a free tool developed by UCSF.

PyMOL. "wizard-mutagenisis". It's very easy.

If you download coot, upload your pdb file and map file, select the command with the radioactive icon on the right hand side of the screen and then click on any residue of your protein it will ask you with which residue you want to replace it and it will try to place it accordingly with the electron density you have. Another option is to go to the "fit loop" menu and select the range of residues you want to change and add the new residues in a single letter code and coot will at the same time replace the aminoacids and fit them for you. it is really easy and straightforward to use. cheers

You may use SPDBV, it is very simple to use, or else Chimera and PyMOL can be used.

Like many others have said, PyMOL is a great option. One word of caution though: if you need to add hydrogens to your structure you may run into problems because PyMOL does not name them properly. The best solution I found for this was to first remove H atoms if necessary, do your mutageneis in Pymol and export the pdb, then load it onto the MolProbity server and fix the H atoms there.

Try Discovery Studio, its easy with GUI based interface.

SwissPDBViewer (sPDBV) might be good tool to change amino acid residues. It is simple and good.

For residues in the protein core, the most accurate results will probably come from SCWRL 4.0, as Stephane suggested. Optimize the mutated residues and all contacting residues, leave the rest untouched (fixed =lowercase in sequence, file moveable= Uppercase). Directly minimizing all residues will cause small changes in all the residues, even those not affected by the mutation. While SCWRL is very good, it is not perfect, and it is probably better to use the native structure as much as possible. You can experiment with how many residues must be optimized upon mutation.

Once finished, you can minimize the energy of the SCWRL structure using GROMACS if you'd like, particularly if it is a low resolution or NMR structure. Directly simulating the structure in GROMACS may not find the optimal energy because many of the sidechains must be moved if the residue is in the protein core, therefore you are likely to hit a local minimum that may be difficult to get out of.

It depends what kind of mutation are you going to perform. If it is to ALA, well just remove the sidechain up top CB in the pdb file (sed can help you in this). If the mutation is in other aa, I use to remove all the sidechain in the pdb file (keeping only CA C N O), rename the aa (i.e. TRP to TYR) in the pdb file and then regenerate the side chain using cns software. Of course, this procedure it is useful if you have to perform either thousand of mutations in your protein (a kind of computational mutation scanning) or the same mutation on thousand of protein files.

Otherwise go with pymol, it is easy.

Use Discovery Studio software where, you can do any type of mutation in amino acid /nucleotide/small molecule as well as you can minimize your particular mutated molecule or complete structure using CHARMM and other force field.

use SCWRL 4.0 it gives best result for mutation. you may do one or more changes to your structure but its advisable to optimize the structure residue wise, when you get mutated sequence you can use any energy minimization packages like gromacs or amber ...

CHARMM program script can do this very easily, you have to read the input structure, pdb and psf, then change the aminoacid sequence of the input to the new one by just replacing the one you want to mutate. Depending on the mutation, you may have to do a few steps minimization of the structure in gas phase, but locally I would advice.

There are many softwares... tryit on pymol

Too many softwares too even list and some of them have already been mentioned by a few people here, but the main issue here is that post replacement which will be the rotamer of your choice. The choice is made by different softwares using a rotamer library. A rotamer library can be backbone-independent, secondary-structure-dependent, or backbone-dependent. Which is why in certain cases especially for eg. for a mutation to an Arg residue the choice is tricky(inside or outside exposed) and can vary from one sofware to another. However, once you choose a particular rotamer you should definitely energy minimize/optimize your structure and if possible run a refinement simulation. In cases where the mutation is highly disruptive you will typically see very high RMSDs even in a short MD sun.

You might want to try MUMBO

http://www.biotechnik.nat.uni-erlangen.de/research/muller/download.shtml

As far as I know, the backbone is kept constant, but the side chains can be exchanged. Then the optimal packing of the new combination of side chains will be calculated.

Hi, try to use the ddg monomer subprogram including in Rosetta 3.4 sofstware, This may you to change any amino acids that you want wtch any other and too minimize the new structure. Also you can use the Pymol interface and change any one that you want, but I recomend you to use Rosetta.

You can use FoldX (http://foldx.crg.es/).

Through the 'PositionScan' and 'BuildModel' functions, you can mutate any residue to any other residue type in your structure, and with the 'alascan' and 'complex' alascan functions you can perform computational alanine scanning mutagenesis trials (for more information on how it is done, and how the software makes sure there are no bad contacts afterwards, refer to the manual/handbook).

The downside is that you will have to work through runfiles and the command line... however, if you are a YASARA user, there is a plugin that provides an interface for most FoldX functions.

You can use Gaussview

charmming.org

Install Discovery studio visualizer (free software) open your structure in that and go to macromolecule , there is one option to mutate the residue so the only thing you have to do is select the residue and mutate it whatever residue you want to.

You can also use Chimera

https://www.cgl.ucsf.edu/chimera/download.html

the subroutine swapaa replaces amino acid sidechains using information from a rotamer library.

https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html

Es.:

swapaa leu :41.a

(change residue 41 in chain A, which is a tryptophan, to leucine)

Luca

I think, you didn't. You should try it again to use swiss pdb view (Spdv). There is mutate option in spdv and you have to click and replace.

You can try SPDV and chimera. Both have sequence editing window where you can simply delete or edit. You can also change from PDB file and edit or delete the amino acid

discovery studio have a program where you can induce the protein mutation.

Try with Foldx. i have already tried for multiple mutations at a time.

VMD ---- Extensions ---- Modelling ---- Mutate Residue

You probably need to load both pdb and psf before use this tool.