Properties of proteins: Difference between revisions

(2 intermediate revisions by the same user not shown)

Line 1:

== Ideal metal bond distances ==

== Ideal metal coordination and bond distances ==

* classic ~~paper~~: Harding, M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins]

* classic papers: Harding, M.M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins]; (2004) [https://doi.org/10.1107/S0907444904004081 The architecture of metal coordination groups in proteins]. The latter has supporting information: zip archive of the website on architecture of metal coordination groups in proteins, and PDFs containing additional tables.

* ~~webservice (2006)~~ http://tanna.bch.ed.ac.uk

* [http://web.archive.org/web/20161031170012/http://tanna.bch.ed.ac.uk/ 2016 archive of original website set up by M. Harding]; MESPEUS database (successor website but also now offline:) [http://web.archive.org/web/20160901002225/http://mespeus.bch.ed.ac.uk/MESPEUS_10/ 2016 archive of website]

* database (~~2008~~) http://~~eduliss~~.bch.ed.ac.uk/~~MESPEUS~~/

* [http://metalweb.cerm.unifi.it/ MetalPDB]

* [https://csgid.org/metal_sites Check my metal]

* see what Martin Maly wrote in https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;979892de.2503 : "consider to try MetalCoord which I wrote about in the thread "3 alternate position of metal ion" from the last week. It can generate restraints for metal-containing monomers. <nowiki>https://github.com/Lekaveh/MetalCoordAnalysis/blob/master/tutorial/tutorial.rst</nowiki> "

== Distinguishing ions from waters ==

Line 20:

Line 22:

that are close to each other should not have an occupancy sum greater

than unity.

Further possibilities:

* From the Phenix package, try: mmtbx.water_screen model.pdb data.mtz elements=NA,K

* WASP analyse water molecules in high-resolution protein structure to check if some of those could be metal ions. WASP could be run as a part of STAN server. STAN - the STructure ANalysis server from USF (http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl )

== Melting point ==

@@ Line 1: / Line 1: @@
-== Ideal metal bond distances ==
+== Ideal metal coordination and bond distances ==
-* classic paper: Harding, M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins]
+* classic papers: Harding, M.M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins]; (2004) [https://doi.org/10.1107/S0907444904004081 The architecture of metal coordination groups in proteins]. The latter has supporting information: zip archive of the website on architecture of metal coordination groups in proteins, and PDFs containing additional tables.
-* webservice (2006) http://tanna.bch.ed.ac.uk
+* [http://web.archive.org/web/20161031170012/http://tanna.bch.ed.ac.uk/ 2016 archive of original website set up by M. Harding]; MESPEUS database (successor website but also now offline:) [http://web.archive.org/web/20160901002225/http://mespeus.bch.ed.ac.uk/MESPEUS_10/ 2016 archive of website]
-* database (2008) http://eduliss.bch.ed.ac.uk/MESPEUS/
+* [http://metalweb.cerm.unifi.it/ MetalPDB]
+* [https://csgid.org/metal_sites Check my metal]
+* see what Martin Maly wrote in https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;979892de.2503 : "consider to try MetalCoord which I wrote about in the thread "3 alternate position of metal ion" from the last week. It can generate restraints for metal-containing monomers. <nowiki>https://github.com/Lekaveh/MetalCoordAnalysis/blob/master/tutorial/tutorial.rst</nowiki> "
 == Distinguishing ions from waters ==
@@ Line 20: / Line 22: @@
 that are close to each other should not have an occupancy sum greater
 than unity.
+Further possibilities:
+* From the Phenix package, try: mmtbx.water_screen model.pdb data.mtz elements=NA,K
+* WASP analyse water molecules in high-resolution protein structure to check if some of those could be metal ions. WASP could be run as a part of STAN server. STAN - the STructure ANalysis server from USF (http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl )
 == Melting point ==