CCP4 wiki - User contributions [en]

Programs for representing the surface of a channel inside protein

2008-08-29T04:08:23Z

Jiamudu:

The following programs can be used for representing the surface of a channel inside protein.

1. PASS.

2. Pymol with Caver scripts. http://www.pymol.org and http://loschmidt.chemi.muni.cz/caver/download.php

3. HOLE. http://d2o.biop.ox.ac.uk:38080/

4. CASTp. http://sts-fw.bioengr.uic.edu/castp/ or http://www.cgl.ucsf.ed/chimera

5. MOLE. http://troll.chemi.muni.cz/whitezone/development/mole/online/moleonline1.3/ or http://mole.chemi.muni.cz/download.php.

6. HOLLOW. http://hollow.sourceforge.net/.

7. The program O can this with following protocol
1/ make object of solvents in the tunnel, sel_off, sel_prop, sel_vis, sphere centred on tunnel...
2/ mask from these solvents, ncs_mask_sph, ncs_mask_lay
3/ asa of just protein
4/ copy space group info from an electron density map to the asa 'map'
5/ average the asa map, using the mask, and IDENT operator, no expansion gives a new map with a surface just around the tunnel.

Programs for representing the surface of a channel inside protein

2008-08-29T04:07:28Z

Jiamudu:

The following programs can be used for representing the surface of a channel inside protein.

1. PASS.

2. Pymol with Caver scripts. http://www.pymol.org and http://loschmidt.chemi.muni.cz/caver/download.php
3. HOLE. http://d2o.biop.ox.ac.uk:38080/

4. CASTp. http://sts-fw.bioengr.uic.edu/castp/ or http://www.cgl.ucsf.ed/chimera

5. MOLE. http://troll.chemi.muni.cz/whitezone/development/mole/online/moleonline1.3/ or http://mole.chemi.muni.cz/download.php.

6. HOLLOW. http://hollow.sourceforge.net/.

7. The program O can this with following protocol
1/ make object of solvents in the tunnel, sel_off, sel_prop, sel_vis, sphere centred on tunnel...
2/ mask from these solvents, ncs_mask_sph, ncs_mask_lay
3/ asa of just protein
4/ copy space group info from an electron density map to the asa 'map'
5/ average the asa map, using the mask, and IDENT operator, no expansion gives a new map with a surface just around the tunnel.

Programs for representing the surface of a channel inside protein

2008-08-29T04:03:17Z

Jiamudu: New page: The following programs can be used for representing the surface of a channel inside protein. 1. PASS. 2. Pymol with Caver scripts. http://www.pymol.org and http://loschmidt.chemi.muni.cz...

The following programs can be used for representing the surface of a channel inside protein.

1. PASS.
2. Pymol with Caver scripts. http://www.pymol.org and http://loschmidt.chemi.muni.cz/caver/download.php
3. HOLE. http://d2o.biop.ox.ac.uk:38080/
4. CASTp. http://sts-fw.bioengr.uic.edu/castp/ or http://www.cgl.ucsf.ed/chimera
5. MOLE. http://troll.chemi.muni.cz/whitezone/development/mole/online/moleonline1.3/ or http://mole.chemi.muni.cz/download.php.
6. HOLLOW. http://hollow.sourceforge.net/.
7. The program O can this with following protocol
1/ make object of solvents in the tunnel, sel_off, sel_prop, sel_vis, sphere centred on tunnel...
2/ mask from these solvents, ncs_mask_sph, ncs_mask_lay
3/ asa of just protein
4/ copy space group info from an electron density map to the asa 'map'
5/ average the asa map, using the mask, and IDENT operator, no expansion gives a new map with a surface just around the tunnel.

Bioinformatics

2008-08-29T03:57:27Z

Jiamudu: /* Structure only */

== Sequence only ==

* [[Servers and programs for sequence analysis]]

== Sequence to structure ==

* [[Prediction of structure from sequence: servers and programs]]

== Structure to Sequence ==

* [[Structure based sequence alignment]]

== Structure only ==

* [[Servers for ligand topologies/parameters]]
* [[Servers for structure analysis|Servers and programs for protein structure analysis]]
* [[Programs for nucleic acid structure analysis|Programs for nucleic acid structure analysis]]
* [[Morphing]]
* [[Programs for representing the surface of a channel inside protein]]

=== Docking ===

* [http://nrc.bu.edu/cluster/ ClusPro] - easy to use web interface
* [http://www.rosettacommons.org/ Rosetta] can do much more than just docking, but is difficult to use
* [http://www.sbg.bio.ic.ac.uk/docking/ 3D-dock] - uses an algorithm that mainly looks at surface complimentarity between the two proteins
* [http://www.csd.abdn.ac.uk/~dritchie/ Dave Ritchie's Hex program] - it is blisteringly quick
* [http://www.nmr.chem.uu.nl/haddock/ Haddock] - recommended by Tassos
* [http://autodock.scripps.edu/ AutoDock] - Wiki at https://www.nbcr.net/pub/wiki/index.php?title=AutoDock

== Other stuff ==

* [[Programs for visualization]] (see also [[Model building]])

* [[Links to Bioinformatics websites]]