Computational Tools in Protein Crystallography (Q37787881)

23 August 2017

title

Computational tools in protein crystallography (English)

1 reference

23 August 2017

Computational Tools in Protein Crystallography (English)

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

11 July 2024

main subject

computational biology

1 reference

Valerie Lamour

2

0 references

Deepti Jain

object named as

Deepti Jain

1

0 references

language of work or name

English

0 references

publication date

1 January 2010

1 reference

full work available at URL

23 August 2017

http://link.springer.com/content/pdf/10.1007/978-1-60761-842-3_8

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Methods in Molecular Biology

11 July 2024

published in

1 reference

23 August 2017

volume

673

1 reference

23 August 2017

page(s)

129-156

1 reference

PHENIX: building new software for automated crystallographic structure determination

23 August 2017

cites work

1 reference

20 May 2022

https://opencitations.net/index/coci/api/v1/citations/10.1107/S0907444902016657

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

1 reference

20 May 2022

https://opencitations.net/index/coci/api/v1/citations/10.1107/S0907444998003254

SuperPose: a simple server for sophisticated structural superposition

1 reference

5 May 2024

https://opencitations.net/index/api/v1/citations/10.1093/NAR/GKH477

Understanding the molecular machinery of genetics through 3D structures

1

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Protein crystallization: from purified protein to diffraction-quality crystal

11 July 2024

2

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

11 July 2024

The phase problem

4

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Advances in direct methods for protein crystallography

11 July 2024

5

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Determination of macromolecular structures from anomalous diffraction of synchrotron radiation

11 July 2024

7

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur

11 July 2024

8

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Resolution of phase ambiguity in macromolecular crystallography

11 July 2024

9

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

The many faces of radiation-induced changes

11 July 2024

10

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

The 'fingerprint' that X-rays can leave on structures

11 July 2024

11

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Structural effects of radiation damage and its potential for phasing

11 July 2024

12

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Processing of X-ray diffraction data collected in oscillation mode

11 July 2024

13

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

The integration of macromolecular diffraction data

11 July 2024

14

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

The CCP4 suite: programs for protein crystallography

11 July 2024

15

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants

11 July 2024

16

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

The finer things in X-ray diffraction data collection

11 July 2024

17

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Choice of data-collection parameters based on statistic modelling

11 July 2024

18

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

A quantitative approach to data-collection strategies

11 July 2024

19

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Solvent content of protein crystals

11 July 2024

20

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals

11 July 2024

21

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

The PredictProtein server

11 July 2024

24

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Comparative protein modelling by satisfaction of spatial restraints

11 July 2024

25

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

The detection of sub-units within the crystallographic asymmetric unit

11 July 2024

26

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Pushing the boundaries of molecular replacement with maximum likelihood

11 July 2024

27

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Likelihood-enhanced fast rotation functions

11 July 2024

28

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

AMoRe: an automated package for molecular replacement

11 July 2024

29

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

MOLREP: an Automated Program for Molecular Replacement

11 July 2024

30

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

[34] Rotation function calculations with GLRF program

11 July 2024

31

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Molecular replacement by evolutionary search

11 July 2024

32

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

MrBUMP: an automated pipeline for molecular replacement

11 July 2024

33

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

BALBES: a molecular-replacement pipeline

11 July 2024

34

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

CaspR: a web server for automated molecular replacement using homology modelling

11 July 2024

35

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

11 July 2024

Molecular replacement

37

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

An open conformation of the Thermus thermophilus gyrase B ATP-binding domain

11 July 2024

39

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Crystallization of the 43 kDa ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin.

11 July 2024

40

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

How Bijvoet made the difference: the growing power of anomalous scattering

11 July 2024

41

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Crystal structure of the catalytic subunit of human protein phosphatase 1 and its complex with tungstate

11 July 2024

42

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Structure-based analysis of catalysis and substrate definition in the HIT protein family

11 July 2024

43

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures.

11 July 2024

44

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Phasing on anomalous signal of sulfurs: what is the limit?

11 July 2024

45

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Screening for phasing atoms in protein crystallography

11 July 2024

46

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

[29] Preparation of selenomethionyl proteins for phase determination

11 July 2024

47

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

CHOOCH: a program for deriving anomalous-scattering factors from X-ray fluorescence spectra

11 July 2024

48

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Substructure solution with SHELXD

11 July 2024

50

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Rapid and automated substructure solution by Shake-and-Bake.

11 July 2024

51

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

SOLVE and RESOLVE: automated structure solution and density modification

11 July 2024

54

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

A flexible and efficient procedure for the solution and phase refinement of protein structures

11 July 2024

57

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

[27] Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods.

11 July 2024

59

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Crystal structure of bacteriophage lambda cII and its DNA complex

11 July 2024

60

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Density modification for macromolecular phase improvement

11 July 2024

61

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Methods used in the structure determination of bovine mitochondrial F1 ATPase

11 July 2024

62

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

SQUASH - combining constraints for macromolecular phase refinement and extension

11 July 2024

64

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Maximum-likelihood density modification

11 July 2024

65

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Automated protein model building combined with iterative structure refinement

11 July 2024

66

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

11 July 2024

67

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Assessment of automatic ligand building in ARP/wARP.

11 July 2024

68

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Automated main-chain model building by template matching and iterative fragment extension

11 July 2024

69

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

11 July 2024

70

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Improved methods for building protein models in electron density maps and the location of errors in these models

11 July 2024

71

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Coot: model-building tools for molecular graphics

11 July 2024

72

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density

11 July 2024

73

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

11 July 2024

ChemDraw Ultra 10.0

74

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Personal experience with four kinds of chemical structure drawing software: review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch

11 July 2024

75

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Crystallographic refinement of ligand complexes

11 July 2024

76

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes

11 July 2024

77

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Refinement of macromolecular structures by the maximum-likelihood method

11 July 2024

79

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

[23] Bayesian statistical viewpoint on structure determination: Basic concepts and examples

11 July 2024

81

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Optimization by Simulated Annealing

11 July 2024

82

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Free R value: cross-validation in crystallography

11 July 2024

86

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Use of TLS parameters to model anisotropic displacements in macromolecular refinement

11 July 2024

87

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

How many water molecules can be detected by protein crystallography?

11 July 2024

88

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Stereochemistry of polypeptide chain configurations

11 July 2024

89

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

PROCHECK: a program to check the stereochemical quality of protein structures

11 July 2024

90

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

11 July 2024

91

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Errors in protein structures

11 July 2024

92

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

11 July 2024

93

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

11 July 2024

94

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

11 July 2024

95

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences

11 July 2024

96

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Touring protein fold space with Dali/FSSP

11 July 2024

97

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

SCOP: a structural classification of proteins database

11 July 2024

98

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

CATH--a hierarchic classification of protein domain structures

11 July 2024

99

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

11 July 2024

100

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

3dSS: 3D structural superposition

11 July 2024

102

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes.

11 July 2024

103

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

RASMOL: biomolecular graphics for all

11 July 2024

105

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

11 July 2024

107

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Reduced surface: An efficient way to compute molecular surfaces

11 July 2024

108

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment

11 July 2024

110

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes

11 July 2024

111

1 reference

https://api.crossref.org/works/10.1007/978-1-60761-842-3_8

11 July 2024

Identifiers

1 reference

23 August 2017

1 reference