Improving published models: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) created page |
Eric Martz (talk | contribs) adding content |
||
| Line 5: | Line 5: | ||
The [http://molprobity.biochem.duke.edu/ MolProbity Server] adds hydrogen atoms (which are missing in most [[X-ray crystallography|crystallographic]] models) and then looks for atomic clashes and analyses the quality of the geometry. Sidechains of Asn, Gln and His often need to be flipped 180 degrees for optimal fit into their immediate environments. Because the electron densities of oxygen and nitrogen are very similar, crystallographers often leave these sidechains in suboptimal positions in published models. MolProbity recommends which sidechains have strong evidence for being in the wrong positions, and offers to flip them to correct the model. | The [http://molprobity.biochem.duke.edu/ MolProbity Server] adds hydrogen atoms (which are missing in most [[X-ray crystallography|crystallographic]] models) and then looks for atomic clashes and analyses the quality of the geometry. Sidechains of Asn, Gln and His often need to be flipped 180 degrees for optimal fit into their immediate environments. Because the electron densities of oxygen and nitrogen are very similar, crystallographers often leave these sidechains in suboptimal positions in published models. MolProbity recommends which sidechains have strong evidence for being in the wrong positions, and offers to flip them to correct the model. | ||
Molprobity's analyses of atomic clashes and geometry are useful in | Molprobity's analyses of atomic clashes and geometry are useful in [[Quality assessment for molecular models|assessing the quality of a model]], overall, and in specific regions of interest, where clashes may be visualized in [[KiNG]]. | ||
==PDB_REDO== | |||
[http://www.cmbi.ru.nl/pdb_redo/ PDB_REDO] does automated re-refinement of published models, and improves about two-thirds of them, according to improvements in [[Free R]]. See the publications linked to the site. [http://www.cmbi.ru.nl/pdb_redo/reprints/nature.pdf Sanderson's succinct overview in ''Nature'', 2009] is a good place to start. | |||
==See Also== | ==See Also== | ||
*[[Quality assessment for molecular models]] | *[[Quality assessment for molecular models]] | ||
