InforLorV4, PascalFrancis, Corpus, bibRecord, 000869

Direct phasing by binary integer programming

Identifieur interne : 000869 ( PascalFrancis/Corpus ); précédent : 000868; suivant : 000870

Direct phasing by binary integer programming

Auteurs : Vladimir Y. Lunin ; Alexandre Urzhumtsev ; Alexander Bockmayr

Source :

Acta crystallographica. Section A, Foundations of crystallography [ 0108-7673 ] ; 2002.

RBID : Pascal:02-0342377

Descripteurs français

Pascal (Inist)
- Etude théorique, Diffraction RX, Résolution structurale, Phase amplitude, Densité électron, Programme ordinateur, Structure cristalline, Protéine, Composé biologique, 6110N.

English descriptors

KwdEn :
- Amplitude phase, Biological compound, Computer program, Crystal structure, Electron density, Proteins, Structure resolution, Theoretical study, XRD.

Abstract

In the absence of phase information, a variety of electron-density distributions is consistent with the observed magnitudes. This ambiguity may be reduced significantly if the distribution values are restricted to 0 or 1, i.e. when the object of search is an envelope rather than a continuous electron-density distribution. The binarizing in both real (the grid-point density values) and reciprocal (the phases) spaces allows the usual structure-factor equations to be replaced by a system of linear inequalities with binary unknowns. A special computer procedure is applied to obtain several sets of values, which satisfy or almost satisfy these inequalities. The averaging of the found phase sets allows the final map to be calculated. The approach was tested with calculated and experimental data for a known protein structure. The size of the grid for the envelope calculation is at the moment the major limitation of the approach. Nevertheless, even for a very small grid, some structure information can be extracted and used as a starting point for further phase improvement or as a way to solve the molecular replacement problem.

Notice en format standard (ISO 2709)

Pour connaître la documentation sur le format Inist Standard.

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A02	`01`			`@0 ACACEQ`
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A05				`@2 58`
A06				`@3 p.3`
A08	`01`	`1`	`ENG`	`@1 Direct phasing by binary integer programming`
A11	`01`	`1`		`@1 LUNIN (Vladimir Y.)`
A11	`02`	`1`		`@1 URZHUMTSEV (Alexandre)`
A11	`03`	`1`		`@1 BOCKMAYR (Alexander)`
A14	`01`			`@1 Institute of Mathematical Problems of Biology, Russian Academy of Sciences @2 Pushchino, Moscow Region, 142290 @3 RUS @Z 1 aut.`
A14	`02`			`@1 LORIA, UMR 7503, Faculté des Sciences, Université Henri Poincaré, Nancy I @2 54506 Vandoeuvre-les-Nancy @3 FRA @Z 1 aut. @Z 3 aut.`
A14	`03`			`@1 LCM3B, UMR 7036 CNRS, Faculté des Sciences, Université Henri Poincaré, Nancy I @2 54506 Vandoeuvre-les-Nancy @3 FRA @Z 2 aut.`
A20				`@1 283-291`
A21				`@1 2002`
A23	`01`			`@0 ENG`
A43	`01`			`@1 INIST @2 5160A @5 354000101369770090`
A44				`@0 0000 @1 © 2002 INIST-CNRS. All rights reserved.`
A45				`@0 18 ref.`
A47	`01`	`1`		`@0 02-0342377`
A60				`@1 P @3 PR`
A61				`@0 A`
A64	`01`	`1`		`@0 Acta crystallographica. Section A, Foundations of crystallography`
A66	`01`			`@0 DNK`
C01	`01`		`ENG`	@0 In the absence of phase information, a variety of electron-density distributions is consistent with the observed magnitudes. This ambiguity may be reduced significantly if the distribution values are restricted to 0 or 1, i.e. when the object of search is an envelope rather than a continuous electron-density distribution. The binarizing in both real (the grid-point density values) and reciprocal (the phases) spaces allows the usual structure-factor equations to be replaced by a system of linear inequalities with binary unknowns. A special computer procedure is applied to obtain several sets of values, which satisfy or almost satisfy these inequalities. The averaging of the found phase sets allows the final map to be calculated. The approach was tested with calculated and experimental data for a known protein structure. The size of the grid for the envelope calculation is at the moment the major limitation of the approach. Nevertheless, even for a very small grid, some structure information can be extracted and used as a starting point for further phase improvement or as a way to solve the molecular replacement problem.
C02	`01`	`3`		`@0 001B60A10N`
C03	`01`	`3`	`FRE`	`@0 Etude théorique @5 01`
C03	`01`	`3`	`ENG`	`@0 Theoretical study @5 01`
C03	`02`	`3`	`FRE`	`@0 Diffraction RX @5 02`
C03	`02`	`3`	`ENG`	`@0 XRD @5 02`
C03	`03`	`X`	`FRE`	`@0 Résolution structurale @5 03`
C03	`03`	`X`	`ENG`	`@0 Structure resolution @5 03`
C03	`03`	`X`	`SPA`	`@0 Resolución estructural @5 03`
C03	`04`	`X`	`FRE`	`@0 Phase amplitude @5 04`
C03	`04`	`X`	`ENG`	`@0 Amplitude phase @5 04`
C03	`04`	`X`	`SPA`	`@0 Fase amplitud @5 04`
C03	`05`	`3`	`FRE`	`@0 Densité électron @5 05`
C03	`05`	`3`	`ENG`	`@0 Electron density @5 05`
C03	`06`	`X`	`FRE`	`@0 Programme ordinateur @5 06`
C03	`06`	`X`	`ENG`	`@0 Computer program @5 06`
C03	`06`	`X`	`SPA`	`@0 Programa computador @5 06`
C03	`07`	`3`	`FRE`	`@0 Structure cristalline @5 07`
C03	`07`	`3`	`ENG`	`@0 Crystal structure @5 07`
C03	`08`	`3`	`FRE`	`@0 Protéine @5 08`
C03	`08`	`3`	`ENG`	`@0 Proteins @5 08`
C03	`09`	`X`	`FRE`	`@0 Composé biologique @5 09`
C03	`09`	`X`	`ENG`	`@0 Biological compound @5 09`
C03	`09`	`X`	`SPA`	`@0 Compuesto biológico @5 09`
C03	`10`	`3`	`FRE`	`@0 6110N @2 PAC @4 INC @5 56`
N21				`@1 189`
N82				`@1 PSI`

Format Inist (serveur)

NO :	PASCAL 02-0342377 INIST
ET :	Direct phasing by binary integer programming
AU :	LUNIN (Vladimir Y.); URZHUMTSEV (Alexandre); BOCKMAYR (Alexander)
AF :	Institute of Mathematical Problems of Biology, Russian Academy of Sciences/Pushchino, Moscow Region, 142290/Russie (1 aut.); LORIA, UMR 7503, Faculté des Sciences, Université Henri Poincaré, Nancy I/54506 Vandoeuvre-les-Nancy/France (1 aut., 3 aut.); LCM3B, UMR 7036 CNRS, Faculté des Sciences, Université Henri Poincaré, Nancy I/54506 Vandoeuvre-les-Nancy/France (2 aut.)
DT :	Publication en série; Papier de recherche; Niveau analytique
SO :	Acta crystallographica. Section A, Foundations of crystallography; ISSN 0108-7673; Coden ACACEQ; Danemark; Da. 2002; Vol. 58; No. p.3; Pp. 283-291; Bibl. 18 ref.
LA :	Anglais
EA :	In the absence of phase information, a variety of electron-density distributions is consistent with the observed magnitudes. This ambiguity may be reduced significantly if the distribution values are restricted to 0 or 1, i.e. when the object of search is an envelope rather than a continuous electron-density distribution. The binarizing in both real (the grid-point density values) and reciprocal (the phases) spaces allows the usual structure-factor equations to be replaced by a system of linear inequalities with binary unknowns. A special computer procedure is applied to obtain several sets of values, which satisfy or almost satisfy these inequalities. The averaging of the found phase sets allows the final map to be calculated. The approach was tested with calculated and experimental data for a known protein structure. The size of the grid for the envelope calculation is at the moment the major limitation of the approach. Nevertheless, even for a very small grid, some structure information can be extracted and used as a starting point for further phase improvement or as a way to solve the molecular replacement problem.
CC :	001B60A10N
FD :	Etude théorique; Diffraction RX; Résolution structurale; Phase amplitude; Densité électron; Programme ordinateur; Structure cristalline; Protéine; Composé biologique; 6110N
ED :	Theoretical study; XRD; Structure resolution; Amplitude phase; Electron density; Computer program; Crystal structure; Proteins; Biological compound
SD :	Resolución estructural; Fase amplitud; Programa computador; Compuesto biológico
LO :	INIST-5160A.354000101369770090
ID :	02-0342377

Links to Exploration step

Pascal:02-0342377

Le document en format XML

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<front><div type="abstract" xml:lang="en">In the absence of phase information, a variety of electron-density distributions is consistent with the observed magnitudes. This ambiguity may be reduced significantly if the distribution values are restricted to 0 or 1, i.e. when the object of search is an envelope rather than a continuous electron-density distribution. The binarizing in both real (the grid-point density values) and reciprocal (the phases) spaces allows the usual structure-factor equations to be replaced by a system of linear inequalities with binary unknowns. A special computer procedure is applied to obtain several sets of values, which satisfy or almost satisfy these inequalities. The averaging of the found phase sets allows the final map to be calculated. The approach was tested with calculated and experimental data for a known protein structure. The size of the grid for the envelope calculation is at the moment the major limitation of the approach. Nevertheless, even for a very small grid, some structure information can be extracted and used as a starting point for further phase improvement or as a way to solve the molecular replacement problem.</div>
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<ET>Direct phasing by binary integer programming</ET>
<AU>LUNIN (Vladimir Y.); URZHUMTSEV (Alexandre); BOCKMAYR (Alexander)</AU>
<AF>Institute of Mathematical Problems of Biology, Russian Academy of Sciences/Pushchino, Moscow Region, 142290/Russie (1 aut.); LORIA, UMR 7503, Faculté des Sciences, Université Henri Poincaré, Nancy I/54506 Vandoeuvre-les-Nancy/France (1 aut., 3 aut.); LCM3B, UMR 7036 CNRS, Faculté des Sciences, Université Henri Poincaré, Nancy I/54506 Vandoeuvre-les-Nancy/France (2 aut.)</AF>
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<LA>Anglais</LA>
<EA>In the absence of phase information, a variety of electron-density distributions is consistent with the observed magnitudes. This ambiguity may be reduced significantly if the distribution values are restricted to 0 or 1, i.e. when the object of search is an envelope rather than a continuous electron-density distribution. The binarizing in both real (the grid-point density values) and reciprocal (the phases) spaces allows the usual structure-factor equations to be replaced by a system of linear inequalities with binary unknowns. A special computer procedure is applied to obtain several sets of values, which satisfy or almost satisfy these inequalities. The averaging of the found phase sets allows the final map to be calculated. The approach was tested with calculated and experimental data for a known protein structure. The size of the grid for the envelope calculation is at the moment the major limitation of the approach. Nevertheless, even for a very small grid, some structure information can be extracted and used as a starting point for further phase improvement or as a way to solve the molecular replacement problem.</EA>
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   |texte=   Direct phasing by binary integer programming
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Direct phasing by binary integer programming

Direct phasing by binary integer programming

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