2fol: Difference between revisions

Revision as of 18:23, 21 February 2008

Crystal structure of human RAB1A in complex with GDP

OverviewOverview

Rapid protein-structure determination relies greatly on software that can automatically build a protein model into an experimental electron-density map. In favorable circumstances, various software systems are capable of building over 90% of the final model. However, completeness falls off rapidly with the resolution of the diffraction data. Manual completion of these partial models is usually feasible, but is time-consuming and prone to subjective interpretation. Except for the N- and C-termini of the chain, the end points of each missing fragment are known from the initial model. Hence, fitting fragments reduces to an inverse-kinematics problem. A method has been developed that combines fast inverse-kinematics algorithms with a real-space torsion-angle refinement procedure in a two-stage approach to fit missing main-chain fragments into the electron density between two anchor points. The first stage samples a large number of closing conformations, guided by the electron density. These candidates are ranked according to density fit. In a subsequent refinement stage, optimization steps are projected onto a carefully chosen subspace of conformation space to preserve rigid geometry and closure. Experimental results show that fitted fragments are in excellent agreement with the final refined structure for lengths of up to 12-15 residues in areas of weak or ambiguous electron density, even at medium to low resolution.

About this StructureAbout this Structure

2FOL is a Single protein structure of sequence from Homo sapiens with , and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Real-space protein-model completion: an inverse-kinematics approach., van den Bedem H, Lotan I, Latombe JC, Deacon AM, Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):2-13. Epub 2004 Dec, 17. PMID:15608370

Page seeded by OCA on Thu Feb 21 17:23:31 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2fol.gif|left|200px]]<br />
+[[Image:2fol.gif|left|200px]]<br /><applet load="2fol" size="350" color="white" frame="true" align="right" spinBox="true"
-<applet load="2fol" size="450" color="white" frame="true" align="right" spinBox="true"
 caption="2fol, resolution 2.631&Aring;" />
 '''Crystal structure of human RAB1A in complex with GDP'''<br />
 ==Overview==
-Rapid protein-structure determination relies greatly on software that can, automatically build a protein model into an experimental electron-density, map. In favorable circumstances, various software systems are capable of, building over 90% of the final model. However, completeness falls off, rapidly with the resolution of the diffraction data. Manual completion of, these partial models is usually feasible, but is time-consuming and prone, to subjective interpretation. Except for the N- and C-termini of the, chain, the end points of each missing fragment are known from the initial, model. Hence, fitting fragments reduces to an inverse-kinematics problem., A method has been developed that combines fast inverse-kinematics, algorithms with a real-space torsion-angle refinement procedure in a, two-stage approach to fit missing main-chain fragments into the electron, density between two anchor points. The first stage samples a large number, of closing conformations, guided by the electron density. These candidates, are ranked according to density fit. In a subsequent refinement stage, optimization steps are projected onto a carefully chosen subspace of, conformation space to preserve rigid geometry and closure. Experimental, results show that fitted fragments are in excellent agreement with the, final refined structure for lengths of up to 12-15 residues in areas of, weak or ambiguous electron density, even at medium to low resolution.
+Rapid protein-structure determination relies greatly on software that can automatically build a protein model into an experimental electron-density map. In favorable circumstances, various software systems are capable of building over 90% of the final model. However, completeness falls off rapidly with the resolution of the diffraction data. Manual completion of these partial models is usually feasible, but is time-consuming and prone to subjective interpretation. Except for the N- and C-termini of the chain, the end points of each missing fragment are known from the initial model. Hence, fitting fragments reduces to an inverse-kinematics problem. A method has been developed that combines fast inverse-kinematics algorithms with a real-space torsion-angle refinement procedure in a two-stage approach to fit missing main-chain fragments into the electron density between two anchor points. The first stage samples a large number of closing conformations, guided by the electron density. These candidates are ranked according to density fit. In a subsequent refinement stage, optimization steps are projected onto a carefully chosen subspace of conformation space to preserve rigid geometry and closure. Experimental results show that fitted fragments are in excellent agreement with the final refined structure for lengths of up to 12-15 residues in areas of weak or ambiguous electron density, even at medium to low resolution.
 ==About this Structure==
-FOL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with MG, GDP and UNX as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FOL OCA].
+FOL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=GDP:'>GDP</scene> and <scene name='pdbligand=UNX:'>UNX</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FOL OCA].
 ==Reference==
@@ Line 18: / Line 17: @@
 [[Category: Edwards, A.]]
 [[Category: Park, H.]]
-[[Category: SGC, Structural.Genomics.Consortium.]]
+[[Category: SGC, Structural Genomics Consortium.]]
 [[Category: Shen, L.]]
 [[Category: Shen, Y.]]
@@ Line 36: / Line 35: @@
 [[Category: structural genomics consortium]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 22:08:27 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:23:31 2008''