I have found Pocket-Finder results very good http://www.modelling.leeds.ac.uk/pocketfinder/

Q-SITE Finder is also good in giving detailed results

through prosite

Qsite finder

I also like Molegro, but it's commercial software....

PyMol can also be helpful with the right plugins.

You might have to go to Sourceforge and get the older copy of PyMOL, as I believe Schrodinger bought it out & commericalized it.

active site atlas

http://www.ebi.ac.uk/thornton-srv/databases/CSA/

For finding the site, as Khawla said you can use prosite (http://prosite.expasy.org/) or maybe the pfam website (http://pfam.sanger.ac.uk/ - click on sequence search) and you get the to the particular amino acids. Then you could load the 3d structure (obtain if from PDB or generate one) into the UCSF Chimera viewer (http://www.cgl.ucsf.edu/chimera/) to see where the residues are and which are nearby in space. Good luck!

I would like to suggest... SiteMap in Schrodinger suit...

I-Tasser website probably among the best to predict binding pocket..

SPRITE/ASSAM - http://mfrlab.org/grafss/sprite/

STING - from EMBRAPA / Campinas - Contact: Dr. Goran Neshich - http://www.cbi.cnptia.embrapa.br/SMS/

with my experience Qsite finder is best one

You mean Active site, then go to the URL: http://www.scfbio-iitd.res.in/dock/ActiveSite.jsp

CASTp calculator is one of the effective online tool to find the catalytic sites of any protein molecules. http://sts.bioengr.uic.edu/castp/calculation.php

hi ,,PyMOL is right choice

Dear Talita, in the database of the NCBI Portal (NIH/NLM), named Protein Clusters (http://www.ncbi.nlm.nih.gov/proteinclusters):

"Entrez Protein Clusters (ProtClustDB). This collection of related protein sequences (clusters) consists of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters. For release-specific information check the stats page.

The Protein Clusters database provides easy access to annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap).

Protein Clusters can be searched like any other Entrez database. For more information on how to use Entrez please examine the Entrez Help Document."

Jess program [5] .....

There was a webinar on imaging 3d ask the expert sriram subraminian who works on cancer

Metapocket is the right choice

Follow this url http://metapocket.eml.org/

Your protein have a 3D model?

there are lots of software available Q-SITE finder is the best one and also PAR -3D, , Meta pocket but Q SITE FINDER is the best one.

Go to www.way2biotech.com and ask the question, you will definitely get a useful answer

http://www.way2biotech.com/replynew.aspx?qid=42&cat=Molecular%20Modeling

try online server catalytic site atlas..................................

http://www.ebi.ac.uk/thornton-srv/databases/CSA/

use CASTp server this one of the best server for catalytic site prediction of protein

Use Castp(Computed Atlas of Surface Topography of Proteins)online server.

Tanq...

I have found Pocket-Finder results very good http://www.modelling.leeds.ac.uk/pocketfinder/

Q-SITE Finder is also good in giving detailed results

catalytic site atlas, PDBSum and CASTp are some of the good ways. Otherwise, if you have the 3D structure of protein bound to ligand, calculating residues within certain distance radius should fetch catalytic site. If you don't have 3D structure, you may align your protein with good homologous structure with ligand and provided that the binding sites are similar, you may derive catalytic site in terms of corresponding residues as well.

Q-site finder uses several separate procedures to perform ligand binding interaction so it is the best software

While several softwares can help you determine the putative binding site.. but remember that the ligand binding site need not always be the catalytic site. You can try Prostie tool (prosite.expasy.org) to determine the active site domain in your protein and then compare it the the available literature. Since several mutation studies are performed on proteins to determine their properties, similar studies must been performed on GSK. An extensive literature review would be of help.

PROSITE, http://prosite.expasy.org/

HMMER

http://hmmer.janelia.org/#download

INTERPROSCAN

www.ebi.ac.uk/Tools/InterProScan

rpi-blast

An useful alternative to the EBI tool (http://www.ebi.ac.uk/thornton-srv/databases/CSA/) is the AutoDock or the AutoDock Vina (free download at: http://autodock.scripps.edu/). All require a .pdb file of the protein, that is the 3-D structure.

A server offering several services is that of the Yang Zhan Lab (http://zhanglab.ccmb.med.umich.edu/). It offers a number of tools. Among them, the I-Tasser provide an "in silico" prediction of the tertiary structure of the protein of interest, and the COFACTOR tool identify functional sites.

Carbana (www.rajasekaran.net.in/tools/carbana.html) is ideal for catalytic site prediction. It works based on carbon distribution. The following two references will help.

1. Prediction of ligand binding sites in globular proteins, R.Senthil, S.Sathish, J.Jannet Vennila and E.Rajasekaran, J. Adv. Bioinfo. Appln. Res. 2(1), 98-99 (2011).

2. Epitope prediction based on carbon content, S. Princeinal Suganthi, S. Shiney Valentina, S. Arul Mugilan and E.Rajsekaran Int. J. Bioinfo.. 4(2), 25-27 (2011).

I would suggest Q-Site finder (http://www.modelling.leeds.ac.uk/qsitefinder/). Also CASTp (http://sts.bioengr.uic.edu/castp/) also provides you a better idea on active site prediction.

You may also go through the text of the PDB file for "HET" atoms. They give you an idea on the active site residues as well.

Or you may try the above mentioned suggestion of ZHANG lab from university of michigan. (http://zhanglab.ccmb.med.umich.edu/) as mentioned by anna giulia. They provide very dependable set of tools for analysis of proteins.

I think SiteMap of Schrodinger software suit will do the job.

Link - https://www.schrodinger.com/products/14/20/

Publications -

1. Halgren, T., "Identifying and Characterizing Binding Sites and Assessing Druggability," J. Chem. Inf. Model., 2009, 49, 377–389

2. Jorgensen, A. M.; Topiol, S., "Driving Forces for Ligand Migration in the Leucine Transporter," Chem. Biol. Drug Des., 2008, 72, 265-272.

3. Halgren, T., "New Method for Fast and Accurate Binding-site Identification and Analysis," Chem. Biol. Drug Des., 2007, 69, 146–148

I wish to inform u to there a many online and offline packages to find catalytic site of the protein..they are...

PyMOL with autodock plugin

Chimera

Discovery Studio "Free Viewer" 2.5.5

MGL tools 1.5

Autodock 4, Autogrid and autodock vina.

And i will give u a link jst check dis out.. http://www.biolib.cz/en/main/

http://www.scfbio-iitd.res.in/bioinformatics/proteinstructure.htm

CSA at the EBI if your structure is known. SitesIdentify web service at the University of Manchester if your protein has reasonable sequence homology to something already in the PDB.

Pocket-picker implemented in pymol or sitemap distribuited by schrodinger; but there are a lot of web-based server that are able to predict the potential active sites of protein

You can try Prostie tool http://prosite.expasy.org/

Http://www.geneinfinity.org/

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

http://www.ncbi.nlm.nih.gov/pubmed/18636476

http://www.jbc.org/content/286/1/674.full

http://pubs.acs.org/doi/abs/10.1021/pr100706k

We do "site-seeking" within TIP: http://eidogen-sertanty.com/products_tip_content.html Happy to run through a few cases with you if you want to give it a try. More info here: http://eidogen-sertanty.com/pubs/siteSeekerwhitePaper.pdf

Hi Talita!!!!!

U may use Q-site finder or SPDBV(Swiss PDB Viewer) for finding catalytic site of the protein of your interest........both of them can be freely downloaded..........

try Amber or Charmm program

pocket finder and Q site finder are good to find catalytic site.

F-pocket, MD Pocket both programs good at finding all possible binding sites in query protein

You can use FTsite.

CASTp is also another tool to find

Q site finder. Http://www.modelling.leeds.ac.uk/qsitefinder/

Castp and Q-site finder are most often used ones. Try out these

Any PDB file (With the presence of a cocrystallized ligand inhibitor) will give you a preliminary idea about the residues of the receptor it is interacting with. Also all PDB files genereally have a term "HET" entry. Which gives you idea about the set of residues that the ligand-receptor interact. This will clearly give you an idea of the active site region or probably should i say the region/residues involved in the interaction. Hope this information was helpful to you.

Yes as others suggested Q-Site and Pocket finder also help you. But they too use the same principle in detecting the active site.

Usually, castp, pocket finder, etc., will shoe us catalytic sites for the structures which were in PDB. Can any one suggest me the tools which show us the catalytic sites for the modelled structures

@Swetha Kumari -- SPRITE will identify similarly arranged amino acid residues - from there you can decide what roles those residues play. The input is a PDB formatted file - can also be modelled structures.

the url http://mfrlab.org/grafss/sprite/

Thank you Mohd Firdaus sir, I will try it today itself.

Thank u Tanima, Bhavaniprasad, and Sabeena . But, @Bhanuprasad, when i tried the modeled structure using MOE in Castp, it didnt accepted.

Catalytic Site Atlas (CSA) : http://www.ebi.ac.uk/thornton-srv/databases/CSA/

I am using METAPOCKET 2.0 online tool ( http://projects.biotec.tu-dresden.de/metapocket/). its provide very good result for our protein structure. this tool had published in journal " Zengming Zhang, Yu Li, Biaoyang Lin, Michael Schroeder and Bingding Huang (2011), Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics, 27 (15): 2083-2088 "

yup METAPOCKET 2.0 online tool ( http://projects.biotec.tu-dresden.de/metapocket/) is very good one

Q-SiteFinder (http://bmbpcu36.leeds.ac.uk/qsitefinder/help.html)

suggesting to use web based software I-Tasser http://zhanglab.ccmb.med.umich.edu/I-TASSER/

Use SiteMap.... schrodinger

http://giribio.weebly.com/xtutorials.html Check this site for more computational biology tools & softwares.

I suggest in order to find potential binding site SiteMap (Schrodinger) and PocketPicker (plugin of PyMOL); but if you search on Internet there are a lot of web-server that are able to perform this type of calculations.

Regards

Wow, thanks for this such very important information :D

u can use either CASTP calculation-Computed atlas of surface topography of proteins or Qsitefinder & Pocket finder.

you can use pocket finderand castP..........

u can use pocketome, q-sitefinder, sitesbase and CASTP to detect catalytic site of protein

From my experience, I would suggest Catalytic site atlas http://www.ebi.ac.uk/thornton-srv/databases/CSA/, Uniprot information about catalytic/binding residues or preferentially HotSpot Wizard http://loschmidt.chemi.muni.cz/hotspotwizard which combines CASTp with some of above-mentioned tools ...

Q-site finder: http://www.modelling.leeds.ac.uk/qsitefinder/

castp, pocket finder, q-site finder or pls have a look a the following link.Hope it would b useful for you

http://bip.weizmann.ac.il/toolbox/structure/binding.htm

In Accelrys Discovery Studio as well, you can predict the binding site cavity.

You might like to try Catalytic Site Atlas http://www.ebi.ac.uk/thornton-srv/databases/CSA/ apart from the structure based prediction models.

Hi,

Plenty of software for that. One more : http://coit-apple01.uncc.edu/MINER/

Hi Talita, u can use Metapocket v2.0 server for active site prediction. It predicts the active site by taking the average of predicted active site of LIGSITEcs, PASS, Q-SiteFinder, SURFNET, Fpocket, GHECOM, ConCavity and POCASA tools.

Hello Talita,

Never depend on any one server as all of them are based on different approaches. Normally i compare results of Castp & pocketFinder. Both of two servers give you idea of pockets i.e. of probable enzymatic sites and not of exact enzymatic sites!!! For exact enzymatic site try PDBsum or CAS (on EBI server), you can get results on these servers if enzymatic site has been reported by any scientist (they dont follow any bioinformatics approach to predict, if know they will tell you).

So best approach is to compare results of Castp, PocketFinder, PDBSum & CAS to conclude best pocket (which can turn into enzymatic site!!!).

And if you are working with Castp& PocketFinder then you don't need to run on any other servers could be Qsitefinder, Fpocket etc.

Also if you are using these sites for docking, then always use more then one site for docking you dont know where you ligand can bind in much better way!! Its more or less like hit-n-trial method.

All the best!

You can use Protein Drug Target Database, in which generally the active site of the protein is defined as all the amino acid residues within 6.5 Å around the bound ligand; however this issue will also depend on the knowledge of the protein (if there are non-synonymous mutations in active site) and above all, the well-known inhibitors (true actives) of your protein. If there is not a large number of them available, I recommend you to check and take into account all of the interacting aminoacids, and if there is a large number do the same but possibly preferring the aminoacids interacting with those ligands having superior binding affinity (nano- or even picomolar).

As per my experience the flowing website will assists you better, I am an user of this tool for the last two years.

http://www.scfbio-iitd.res.in/dock/ActiveSite.jsp

A few also you find in EXpassy

Hi friend,

My suggestion is to go and visit catalytic site atlas (CSA) which gives you absolute catalytic triad of the enzyme. Good luck !

Hey Talita,

I'd go for Q-site finder or Swiss PBD Viewer. Both of 'em are freewares and you can easily download 'em........

Hope this was helpful!!!

Q-site ,pocket finder, incasitefinder n poctetome ..... are good to find catalytic sites.

Dear Talita,

You may want to try this two sites:

Fun fold: will find possible ligand binding pockets in your sequence using the amino acid sequence. Has a large degree of uncertainty.

http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form.html

SVMprot will try to find similarity patters to classify your protein into a functional protein family, from there you could search for relatives in the PDB and see how the ligands do bind.

http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi

The third approach might be, if you know the ligand of your protein (substrate) go to the PDB and in the top search BOX you will find ligand. click on the ligand icon and type your ligands name. As you type you will see suggestions. You may type a full name or part of it. If you type part you will widen your search if you type the full name your search will be narrowed down to really similar molecules. i.e. if your ligand is NAD+ you may type NAD, you may type adenine, you may type nicotinamide or both (nicotinamide adenine).

Then you will have a list of structures where the ligand of the ligands moiety is found. Showing you the structure on the left.

Review the list carefully, find those ligands more closely resembling your ligand. Click on the structures where those closely related molecules are found. On each structure's page, you will see a list of ligands found in that structure. Use ligand explorer (there is a box on the right side of the row of each ligand click on the word ligand explorer). Allow the software to install in your computer (it is safe, computer virus free). Use the software to see how it binds. Compare to your protein to see if you can find similar sites.

This last approach is truly tough work, but it may render very nice results.

Best wishes,

Rogelio

For proteins that have been studied previously, or are very similar to those studied previously, use the Catalytic Site Atlas: http://www.ebi.ac.uk/thornton-srv/databases/CSA/ You can enter a code or an EC number and it returns a list of residues that are either known to be catalytically important (and it gives the references) or the residues that are aligned with the known catalytic residues in a previously studied protein. For proteins where there are no direct experimental data available, submit the structure (or a model structure) to the POOL server: http://www.pool.neu.edu/wPOOL/ POOL combines electrostatic information with surface geometric and (optional) phylogenetic information for very accurate active site residue prediction. References are given at the website.

All these server give you a cavity of protein, but my suggestion go for manual method, do the balst of your protein and identify the high identical structure and go for multiple sequence alignment; from that you can identify the possible high conserve residues; based on the solved structures you can easily identify the active site residue more perfectly then the software or server prediction methods

Have someone used pocket results of PDBSUM!!

Talita,

You can use Fpocket (C/C++ compiled program) or MSpocket (python scripts) to obtain PDB files from your predicted pockets.

No - the POOL server is not a pocket finder. It uses electrostatic and chemical properties and is very accurate. It is based on the structure of the query protein. See: https://www.researchgate.net/publication/225095730_POOL_server_machine_learning_application_for_functional_site_prediction_in_proteins

The POOL server is much more precise than a simple pocket finder.

Article POOL server: Machine learning application for functional sit...

Recently we posted a new Catalytic Site Atlas (CSA) database search tool. Please check it out at http://catsid.llnl.gov/ and let me know if it is useful for you.

Try this

www.scfbio-iitd.res.in/dock/ActiveSite.jsp

Jim Warwicker's group at the University of Manchester created a web server SitesIdentify (REF http://genomebiology.com/1471-2105/10/379/citation) http://www.manchester.ac.uk/bioinformatics/sitesidentify/ which is an electrostatics tool for finding and characterising cavities in protein surfaces likely to constitute active sites or binding sites. It was developed using data taken from CSA.