Re: [ccp4bb] binding pockets...
Hi This was brought to my attention after I posted yesterday, to add to the list I sent then - pyvol - Python (as a PyMol plug-in, a python module and as a command-line Python script) - needs a config file to run - https://schlessinger-lab.github.io/pyvol/index.html The output is the surface of the pocket as vertices and faces in a file with the extension “.obj” (the other programs fill the pocket with dummy atoms). Result looks most similar to that from parKVFinder. Again, many thanks for the input Harry > On 12 Jan 2023, at 11:26, Harry Powell wrote: > > Hi folks > > a round-up of what I’ve found - four examples that I can run from the > command-line. > > fpocket - mostly C, C++ - https://github.com/Discngine/fpocket > > ghecom - C - https://pdbj.org/ghecom/ > > parKVFinder (replaces KVFinder, also available as a Python module) - Python:C > 60:40 - https://github.com/lbc-lnbio/parkvfinder > > p2rank - Groovy, Java (won't run with Java 19 on my High Sierra box, works > with Java 17) - https://github.com/rdk/p2rank > > and some screenshots (from QtMG) of the surface of the largest pocket found > by each (using default settings) for the polypeptide from chain A of 1A9W (a > haemoglobin) I’ve removed all HETATMs from this before running the progs) > superimposed over the haem (or heme, if you prefer ;-)) - in the order of the > programs given above - > > > > Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] binding pockets...
Hi Mike Interesting. I haven’t looked at Java stuff for quite some time… Harry > On 4 Jan 2023, at 12:53, Mike S wrote: > > Have you tried P2Rank? It is quite fast, and there is a standalone version > that has command line options to run against all coordinate files in a > directory using batch mode. > > https://prankweb.cz/ > https://prankweb.cz/about > https://github.com/rdk/p2rank > > You can try the web version to see how it performs with one of your > favorites. I like the automatically created pymol scripts as well. It does > occasionally split a larger pocket into smaller ones, similar to the fpocket > behavior, but perhaps not quite as frequent. > > -Mike > > On Wed, Jan 4, 2023 at 6:31 AM Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > THX for the replies - > > > On 3 Jan 2023, at 22:56, Bernhard Rupp wrote: > > > > There is also a service from our Polish friends: > > called Spaceball (jokes aside) that calculates the volume of protein > > cavities (http://www.ifpan.edu.pl/~chwastyk/spaceball/). > > and the services in Hamburg are useful for visualization of binding pockets > > and channels > > https://proteins.plus/ > > I really want something that I can put iin a script, not a web-page. These > both appear to be web interfaces > > > James Holton - > > > > PanDDA? > > PanDDA is really for density analysis across putative changed-state datasets > - I have many thousands of models to inspect that have no associated > experimental datasets > > > Andre Godoy - > > > > if you mean predicting binding sites, FT map is quite good > > > > Unfortunately another web interface - http://ftmap.bu.edu/serverhelp.php > > I’m really after alternatives to programs like: > > pyKVFinder (but that won’t install easily from PYPI on my Mac because > my OS is too old - if anyone wants to buy me a new big, fast Mac to replace > my old, fast Mac I should be able to install that easily!!) or > > fpocket (which works okay but is splitting up “obvious" single-site > pockets into multiple pockets). > > Plus they need to be able to run from a script (or from the command-line so > it can be scripted) - web interfaces are okay if you have a few examples, but > when you’re analysing 1000 - 1500 models a day, clicking buttons gets a > little boring! > > Sorry my initial post wasn’t clearer > > Harry > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] binding pockets...
Have you tried P2Rank? It is quite fast, and there is a standalone version that has command line options to run against all coordinate files in a directory using batch mode. https://prankweb.cz/ https://prankweb.cz/about https://github.com/rdk/p2rank You can try the web version to see how it performs with one of your favorites. I like the automatically created pymol scripts as well. It does occasionally split a larger pocket into smaller ones, similar to the fpocket behavior, but perhaps not quite as frequent. -Mike On Wed, Jan 4, 2023 at 6:31 AM Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > THX for the replies - > > > On 3 Jan 2023, at 22:56, Bernhard Rupp wrote: > > > > There is also a service from our Polish friends: > > called Spaceball (jokes aside) that calculates the volume of protein > cavities (http://www.ifpan.edu.pl/~chwastyk/spaceball/). > > and the services in Hamburg are useful for visualization of binding > pockets and channels > > https://proteins.plus/ > > I really want something that I can put iin a script, not a web-page. These > both appear to be web interfaces > > > James Holton - > > > > PanDDA? > > PanDDA is really for density analysis across putative changed-state > datasets - I have many thousands of models to inspect that have no > associated experimental datasets > > > Andre Godoy - > > > > if you mean predicting binding sites, FT map is quite good > > > > Unfortunately another web interface - http://ftmap.bu.edu/serverhelp.php > > I’m really after alternatives to programs like: > > pyKVFinder (but that won’t install easily from PYPI on my Mac > because my OS is too old - if anyone wants to buy me a new big, fast Mac to > replace my old, fast Mac I should be able to install that easily!!) or > > fpocket (which works okay but is splitting up “obvious" > single-site pockets into multiple pockets). > > Plus they need to be able to run from a script (or from the command-line > so it can be scripted) - web interfaces are okay if you have a few > examples, but when you’re analysing 1000 - 1500 models a day, clicking > buttons gets a little boring! > > Sorry my initial post wasn’t clearer > > Harry > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] binding pockets...
THX for the replies - > On 3 Jan 2023, at 22:56, Bernhard Rupp wrote: > > There is also a service from our Polish friends: > called Spaceball (jokes aside) that calculates the volume of protein cavities > (http://www.ifpan.edu.pl/~chwastyk/spaceball/). > and the services in Hamburg are useful for visualization of binding pockets > and channels > https://proteins.plus/ I really want something that I can put iin a script, not a web-page. These both appear to be web interfaces > James Holton - > > PanDDA? PanDDA is really for density analysis across putative changed-state datasets - I have many thousands of models to inspect that have no associated experimental datasets > Andre Godoy - > > if you mean predicting binding sites, FT map is quite good > Unfortunately another web interface - http://ftmap.bu.edu/serverhelp.php I’m really after alternatives to programs like: pyKVFinder (but that won’t install easily from PYPI on my Mac because my OS is too old - if anyone wants to buy me a new big, fast Mac to replace my old, fast Mac I should be able to install that easily!!) or fpocket (which works okay but is splitting up “obvious" single-site pockets into multiple pockets). Plus they need to be able to run from a script (or from the command-line so it can be scripted) - web interfaces are okay if you have a few examples, but when you’re analysing 1000 - 1500 models a day, clicking buttons gets a little boring! Sorry my initial post wasn’t clearer Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] binding pockets...
There is also a service from our Polish friends: called Spaceball (jokes aside) that calculates the volume of protein cavities (http://www.ifpan.edu.pl/~chwastyk/spaceball/). and the services in Hamburg are useful for visualization of binding pockets and channels https://proteins.plus/ Best, BR On 1/3/2023 7:14 AM, Harry Powell wrote: > Hi folks > > I was wondering what people’s favourite program is to find binding pockets in > proteins. I’ve had a look at a couple but each has its own idiosyncrasies. > > HNY > > Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] binding pockets...
Hi Harry if you mean predicting binding sites, FT map is quite good Andre S. Godoy, PhD Universidade de São Paulo Instituto de Física de São Carlos Av. João Dagnone, 1100, Jd. Santa Angelina13563-120 - São Carlos, SP, Brazil Em terça-feira, 3 de janeiro de 2023 12:15:19 BRT, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> escreveu: Hi folks I was wondering what people’s favourite program is to find binding pockets in proteins. I’ve had a look at a couple but each has its own idiosyncrasies. HNY Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] binding pockets...
PanDDA ? On 1/3/2023 7:14 AM, Harry Powell wrote: Hi folks I was wondering what people’s favourite program is to find binding pockets in proteins. I’ve had a look at a couple but each has its own idiosyncrasies. HNY Harry To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
