PyMOL does the RMS comparison very easily. I'd do it there. Or you can write a script to read the coordinates for the respective pdb files and do an RMS calculation.

Hi Martin, try the DALI server:

http://protein.hbu.cn:83/fssp/www.ebi.ac.uk/dali/index.html

Use RasMol

http://www.umass.edu/microbio.rasmol/

or you can use VMD

Chimera have such option. u can view, superimpose both structurally and multiple sequence alignment. secondary structural analysis etc

Hello, Martin.

For pure 3D, do it with your favorite viewer (mine is UCSF Chimera www.cgl.ucsf.edu/chimera/).

For more bifo work with some 3D capacities I would definitively go for swiss-pdbviewer (http://spdbv.vital-it.ch/)

You can also use Coot.

Try msTALI : http://ifestos.cse.sc.edu/software.php#mstali

It aligns multiple structures based on their torsion angles, accessibility, sequence similarity and other stuff.

You can use webserver POSA or Matt, these two web servers also provide excutable code for Linux system.

The best for the potential is swiss pdbviwer. You can work with two structures at time and tool the structures very easy

use MultiProt

http://bioinfo3d.cs.tau.ac.il/MultiProt/

PyMOL does the RMS comparison very easily. I'd do it there. Or you can write a script to read the coordinates for the respective pdb files and do an RMS calculation.

As Oscar Huertas, I suggest to use the pdbviewer software (http://spdbv.vital-it.ch/). It is easy to use and allow the comparison of pdb and to use the 3D structure as template for your gene of interest. After if you want to make a deepest analysis (molecular replacement), it would preferable to use other software (as Pymol, that it used by structural specialist in my lab).

It depends upon your need. What do you wanna perform....for multiple sequence analysis of PDb structures you may perform a simple BLASTp against PDB database. If you wanna compare at structural level you may use Swiss-PDBviewer (Free software) or you may also try Schrodinger modules (Commercial package). I guess Python based Modeller (Academic software) also may help you for performing homology modelling using multiple PDB templates.

I preffer use PyMol, some tools are very good for research in proteins.

Try chimera http://www.cgl.ucsf.edu/chimera/ It's free and you can do a match/align like in other software and get an RMSD between a set of structures.

You say you want to compare it with a high percentage? Of what? Are we talking about the sequence, I assume?

Chimera is your best bet probably as it will bring up the sequences from the PDB structures you've loaded and let you align them and it will show secondary structure on the sequence next to the actual visualisation of the molecules.

Try VMD www.ks.uiuc.edu/Research/vmd/

It's free and by using some simple selection commands you can visualize different PDBs

Pymol is a good tool for work. you can compare and put one over the other too ...

What do you need? Compare pdb files for.....

CCP4 COOT should have an RMSD facility for comparing structures. But I would use PyMOL like many of the others suggest.

VMD ( http://www.ks.uiuc.edu/Research/vmd/ ) has an evolutionary analysis environment, MultiSeq ( http://www.scs.illinois.edu/schulten/multiseq/ ), that can handle structure and sequence alignments as well as tree drawing based on both sequence and structure metrics. Also, if you load up PDB files, all sorts of metadata will be available such as lineage information, E.C. number, etc. There are extensive tutorials available for VMD ( http://www.ks.uiuc.edu/Training/Tutorials/#vmd ) including some specific to MultiSeq ( http://www.scs.illinois.edu/schulten/tutorials/index.html ).

We do this all the time at the sequence, structure, and site level. It is very likely we have the comparisons in TIP already, and if not, can readily trigger the calculation of any thing that might be missing. See this: http://eidogen-sertanty.com/products_tip_content.html. Also see this: http://www.eidogen.com/pubs/acs-30aug2011-proteinmining.pdf If you just have a few you want to check-out, drop me a line. I can pull a few for you.

Pymol, definitely!

I prefer PyMOL ( http://pymol.org ) - Download structures > A (align)>to molecule>"specify a structure for comparing" = something like this:

Match: read scoring matrix.

Match: assigning 357 x 261 pairwise scores.

MatchAlign: aligning residues (357 vs 261)...

ExecutiveAlign: 250 atoms aligned.

ExecutiveRMS: 17 atoms rejected during cycle 1 (RMS=1.76).

ExecutiveRMS: 10 atoms rejected during cycle 2 (RMS=1.29).

ExecutiveRMS: 3 atoms rejected during cycle 3 (RMS=1.11).

ExecutiveRMS: 2 atoms rejected during cycle 4 (RMS=1.08).

ExecutiveRMS: 1 atoms rejected during cycle 5 (RMS=1.07).

Executive: RMS = 1.062 (217 to 217 atoms)

Executive: object "aln_2gu8_to_1mq4" created.

+ Graphical presentation of aligned structures.

Accelrys Discovery Studio (visualiser) - http://accelrys.com/products/discovery-studio/ and VMD (http://www.ks.uiuc.edu/Research/vmd/ ) also work...

Vmd or pymol

Hi...Martin, actually there are many tools for superimpose, you can check all of of them. I suggest you to try STRAP java for comparing multiple PDB. check this link http://www.charite.de/bioinf/strap/Scripting.html

Try VAST at NCBI.. This tool has already pre-computed 3D alignments of related protein structures in PDB Iconverted to NCBIs MMDB). You can superimpose as many as you like in a 3D view using CN3D. It is very easy and rapid, since the alignments are pre-computed.

I know you can open serveral PDB in the Swiss-Pdbviewer (http://expasy.org/proteomics). IT might help you out....

You can use Swiss-Pdbviewer.

I prefer BALLView (http://www.ball-project.org/Ballview).

It offers intuitive handling as well as a python scripting interface.

Pymol, which is easy scriptable and useful.

STRAP, groups several tools for prediction, superimpose, blast, manipulated and visualisation 3D structure...including pymol expasy uniprot DALI....

http://www.charite.de/bioinf/strap/Scripting.html

A+

What you want to do is already implemented in multiseq (http://www.ks.uiuc.edu/Research/vmd/plugins/multiseq/), running under VMD (http://www.ks.uiuc.edu/Research/vmd/)

Dear Martin Banchero,

Dear Martin Banchero ,

DALI Database

The Dali Database is based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank* (PDB).

http://ekhidna.biocenter.helsinki.fi/dali/start

DMAPS

DMAPS database contains pre-computed multiple structure alignments for protein chains in the Protein Data Bank (PDB). Automated structure alignments have been generated for classified protein families using CE-MC algorithm.

http://bioapps.rit.albany.edu/DMAPS/

DBAli

A Database of Structure Alignments.

http://salilab.org/DBAli/

VAST

Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one.

http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

FSSP

FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB).

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+FSSP

Finally I use the SSAP server from CATHdb because it compares the PDBs taking into account the separate domains also returns the data that I need as rmsd, seq_id (%), overlap, etc.

The only disadvantage is that you can not simultaneously compare all PDBs but rather to be compared in pairs making it is somewhat tedious.

you can use Discovery studeo...

we have recently used pymol in this semester and i think it can be used for multiple PDB files at a time.I don't know much of it.we used it to align PDB files of three proteins whose structures are known with the comparative model of another protein whose structure was unknown.we performed the analysis using the four PDB files at a time.

i dont think pymol could be suitable tool

hi u can use pymol,swisspdbviewer etc.

In the table on http://en.wikipedia.org/wiki/Structural_alignment_software you have the "Type" column specifying whether the software can compare multiple structures. I would suggest trying more than one option and compare the results . You may try first with MAMMOTH and MultiProt.

Hi you can use STRAP..

Hi,

Depending on your need you should use the structure alignment software.

if you want the structural comparision based on SSE (Secondary Structure Elements Alignmen) you can use Mass (http://bioinfo3d.cs.tau.ac.il/MASS/) or if you want it to be based on Cα (Backbone Atom (Cα) Alignment) you can use STRAP (http://3d-alignment.eu/) .

You can have the list of software from wikipedia (http://en.wikipedia.org/wiki/Structural_alignment_software) and you can also see the basis on which the structural alignment is done.

Hope it helps.

Hi, I would definitively recommend swiss-pdbviewer and its "Magic Fit" function that works very fine for a rapid yet meaningful overlap of protein 3D structure. http://spdbv.vital-it.ch/ Enjoy!

A very complete list of modeling softwares/webservices at www.click2drug.org. Enjoy this on as well!

Hi Martin, I would also try MAMMOTH (http://ub.cbm.uam.es/software/online/mamothmult.php) a tool designed for multiple structure alignment. You can read about it in Lupyan D, Leo-Macias A, Ortiz AR (2005) Bioinformatics (2005) 21, 3255-63. We have used it with good results. I suggest that before you use it (or any other structure alignment software) you check you PDB files, and may be clean them from what you do not want to be aligned (e.g. extra chains). Of course, if this work is a central part of a project I would try several programs. Finally, I have to say that I assume you are aligning homologs and not replicas of the same structure. Good luck !

There's another path. You can merge this structures in a trajectory file using g_trjcat program of GROMACS package. So, you'll can perform several types os comparative analysis between this structures. It's not so fast, but work well!

I usually use UCSF Chimera to do it!

Pymol or SPDBV both are good... i personally use pymol

Keep in mind that PyMOL does an iterative atom removal during its `fit` command. You can tell it not to be smart about it by specifying 0 as your third parameter: `fit pdb1, pdb2, 0`

I'm agree I use Pymol for the comparison or SPDBViewer ...actually Vector NTI has a complement for 3D analysis but I don't nknow if is good enough

I will sugest DALI, the server will do everything for you:

"The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB)."

http://ekhidna.biocenter.helsinki.fi/dali_server/start

Hi Martin,

Your question is quite elusive to me

"check if their structures are related to a really high percentage"

On what basis do you want to compare the structures, and on what do you want to perform a percentage.

Many people already suggested you tools to perform structure superimposition with RMSD computation, this can be a good solution indeed.

If this is not accurate enough to answer your question, I suggest MODELLER, and its SALIGN module. SALIGN has this advantage to take into account various sequence an structural elements in the alignment process as well as in the scoring. And if you are not convinced by the respective weights given to these elements in the computation, you can tweak them. Moreover, you can code and provide your own criteria of fit.

MODELLER's main page : http://salilab.org/modeller/about_modeller.html

If you want to check the trajectories of pdb structures i.e. keeping one pdb file as reference structure and compare all the structures with the reference structure then there are many programs and softwares to do that

like VMD, gromacs, Discovery Studio, Profit, Pymol..

There are many more, based on your requirement and access, you have to make the choice.

SPDBV have such option.

I generally use either SPDV or PyMol as one can compare more than 2 structures simultaneously. However, for comparing 2 structures there several online comparison tools one found on PDB website itself

I prefer to use Pymol or SPDBV. why you are using pdb file, instead if you have aa sequence you can do many methods in Bioedit

Yes. pymol alignment had almost similar RMS value compared to Dali server

Hi Martin,

I'm sorry but I should say your question should be little more elaborative to get a proper answer.

You have asked to compare multiple PDBs, but didn't clarify the fact that you have/download all those PDB files or you wanna extract homologous PDB files from rcsb through comparing the structure of your interest.

If the first case is true, I think you already have your answer. Yes, you have to align related structures and the softwares which are good for this purpose are,

A) COOT & O both are very popular software used mainly by structural biologists. If you know how to use them they are simply the best.

B) If you are not a structure person, I think Chimera, PYMOL, SPDB Viewer, VMD are the software you would be interested. They are command friendly and although you couldn't align them according to your choice ( which you could do in COOT or O), they are good enough for basic structural studies.

But, if you are looking for the 2nd case, none of them would be your answer.

Then you should do,

A) Go to this site http://www.ebi.ac.uk/msd-srv/ssm/ and submit your structure.

B) Do Protein- Blast search (http://blast.ncbi.nlm.nih.gov/), by choosing the database PDB would give you a collection of sequences similar to yours with their structures.

I believe you might want to superimpose the 3D-structures. If so, I like MULTIPROT (http://bioinfo3d.cs.tau.ac.il/MultiProt/). I have used it to superimpose the 3D structure of 20 different proteins. From the superimposed structures you can get a MSA using the program STACCATO.

Using spdbv scripting might do the work

T-Coffee has a special mode named EXPRESSO, to build structure based multiple sequence alignments. IF you provide a FASTA of the PDB structures, it will fetch the structures itself (you can also feed the stuctures directly in the advanced mode)

http://tcoffee.crg.cat/apps/tcoffee/do:expresso

there are many software are available like VMD , SPDBV , chimera, COOT etc.

Http://www.bioinformatics.org/strap/

Submit your coordinates to http://flensburg.zbh.uni-hamburg.de/~wurst/salami/

This will find structurally related PDB files and give you rather good superpositions, regardless of how weak the sequence identity is.

It will also let you see the alignment in fasta format.

If you get enthusiastic, you can also download the code for pairwise alignments.

If you have high sequence identity, then just use something like chimera's matchmaker function.

MultiProt is good, and I think it's fit for your objective. It was developed by Dr. Maxim Shatsky in Wolfson's and Nussinov's lab. You can choose sequence-dependent or sequence-independent manner, depending on the sequence constraint or merely the structural similarity without restriction of sequence. From the results you'll find how many percentages of the proteins and which regions have similar structure.

Yes you can go with Spartan

for more details regarding spartan in terms of your asked query for multiple PDBs comparison you can mail me [email protected] will definitely come up with exact solution.

One way to compare two proteins that are similar is apply protein blast as Saugata Hazra posted.

Pymol and Chimera, both of these visualization softwares will be handy to compare a number of proteins - where they can be aligned and their structural differences, sequencial differences can be noted easily and their rmsd can be calculated aligning over each other.

Moe

PyMol can do the job

Discovery studio visualiser can also do the job

Most structure alignment programs use rigid body superposition. This may prove problematic even for the same protein in two different conformations (for instance, ligand bound and unbound structures). We use Matt (http://groups.csail.mit.edu/cb/matt/) or DALI (http://ekhidna.biocenter.helsinki.fi/dali_server) to compare protein structures because they take a fragment based approach. One other program that uses both structure and sequence similarity is DeepAlign (http://ttic.uchicago.edu/~jinbo/software.htm) which aligns structures with sequence identity as low as 5-10%.

Pymol can be the best software for the comparision of multiple protein structures. Chimera also serves better for this one. Even the sequences can be aligned and compared for your purpose.

Hi all,

Could someone please suggest some software for superposing DNA 3D structures. Pymol and chimera are not able to do the same.

Regards,

Nutan

Discovery Studio Viewer Pro will be used for superposing function.

SwissPDBviewer was also be used for superposing DNA.

SwissPDBviewer or go to expasy you will get lot of tools there for your purpose.

Dali server ... CLIQUE superposition ...

This function is implemented in most of visualizers. And some of them have been already mentioned. Personally, I give my vote for PyMOL. Although I work with most of these programs, in my opinion PyMOL is the most intuitive ...

you can also try visual molecular dynamics (VMD), which is freely downloadable from the web

STRAP integrates several viewer and structural modelling programs and simple sequence alignment algorithms.

http://www.bioinformatics.org/strap/

The Best!

REMEMBER I HAVE SUPERPOSED TWO STRUCTURES FOR ANALYSIS. I FOUND TWO DIFFERENT RESULT FROM TOP TWO SOFTWARE, 'MOE' AND 'PYMOL'

I though this thread was dead... It is so old.

Yet one comment regarding the last contribution by Muhammad Khan:

All comparison methods are based on assumptions are use different algorithmic approaches. Ever pretty automatic tools, like PyMol or spdbv, relay on specific considerations and take internal "decisions" to perform the structural alignment. It is unlikely two different tools will give the exact same results.

Having said that, and after going through the whole thread again, I summarized the software (mostly molecular viewers) mentioned throughout:

(~by number of mentions, but not a rigorous count)

PyMol - https://pymol.org/

STRAP java - http://www.charite.de/bioinf/strap/Scripting.html

UCSF Chimera - http://www.cgl.ucsf.edu/chimera/

DALI - http://protein.hbu.cn:83/fssp/www.ebi.ac.uk/dali/index.html

swiss pdbviwer - https://spdbv.vital-it.ch/

VMD - https://www.ks.uiuc.edu/Research/vmd/

MULTIPROT – http://bioinfo3d.cs.tau.ac.il/MultiProt/

MAMMOTH – http://ub.cbm.uam.es/software/online/mamothmult.php

COOT - https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

msTALI - http://ifestos.cse.sc.edu/software.php#mstali

Discovery Studio, ArgusLab or LigandScout

Schrödinger's Maestro – https://www.schrodinger.com/maestro

BALLView – http://www.ball-project.org/Ballview

GROMACS tools - http://www.gromacs.org/

T-Coffee special mode EXPRESSO – http://tcoffee.crg.cat/apps/tcoffee/do:expresso

SALAMI – http://flensburg.zbh.uni-hamburg.de/~wurst/salami/

Matt – http://groups.csail.mit.edu/cb/matt/

RASMOL - http://www.umass.edu/microbio.rasmol/

LINK TO MANY – http://en.wikipedia.org/wiki/Structural_alignment_software

Best wishes,

Rogelio

Three best software when i worked after dozen of time practice and observations and analysis, i found that chimera and MOE work best in this regards. pymol was found in with different result