4.4 Article

PDB_REDO: constructive validation, more than just looking for errors

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

To B or not to B: a question of resolution?

Ethan A. Merritt

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2012)

Article Biochemical Research Methods

REFMAC5 for the refinement of macromolecular crystal structures

Garib N. Murshudov et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Biochemical Research Methods

Overview of the CCP4 suite and current developments

Martyn D. Winn et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)

Article Biochemical Research Methods

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

Robbie P. Joosten et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

Gaia: automated quality assessment of protein structure models

Pradeep Kota et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Proteopedia: A status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules

Jaime Prilusky et al.

JOURNAL OF STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

A series of PDB related databases for everyday needs

Robbie P. Joosten et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

Structural basis for the sequence-specific recognition of human ISG15 by the NS1 protein of influenza B virus

Rongjin Guan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemistry & Molecular Biology

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

Randy J. Read et al.

STRUCTURE (2011)

Article Biochemical Research Methods

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Chemistry, Multidisciplinary

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

Pavel V. Afonine et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2010)

Article Biochemistry & Molecular Biology

Functional Analysis of the Kv1.1 N255D Mutation Associated with Autosomal Dominant Hypomagnesemia

Jenny van der Wijst et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2010)

Article Biochemical Research Methods

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

Robbie P. Joosten et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2009)

Article Chemistry, Multidisciplinary

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Robbie P. Joosten et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2009)

Article Biochemistry & Molecular Biology

Remediation of the protein data bank archive

Kim Henrick et al.

NUCLEIC ACIDS RESEARCH (2008)

Letter Multidisciplinary Sciences

PDB improvement starts with data deposition

Robbie P. Joosten et al.

SCIENCE (2007)

Article Biochemistry & Molecular Biology

β-edge interactions in a pentadecameric human antibody Vκ domain

Leo C. James et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Artemin crystal structure reveals insights into heparan sulfate binding

L Silvian et al.

BIOCHEMISTRY (2006)

Article Biochemical Research Methods

Optimal description of a protein structure in terms of multiple groups undergoing TLS motion

J Painter et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2006)

Article Chemistry, Multidisciplinary

Electron transfer between cytochrome c and cytochome c peroxidase in single crystals

SA Kang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Biochemical Research Methods

REFMAC5 dictionary:: organization of prior chemical knowledge and guidelines for its use

AA Vagin et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)

Article Biochemical Research Methods

The Uppsala Electron-Density Server

GJ Kleywegt et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)

Article Biochemical Research Methods

Coot:: model-building tools for molecular graphics

P Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2004)

Article Biochemistry & Molecular Biology

MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes

IW Davis et al.

NUCLEIC ACIDS RESEARCH (2004)

Letter Biochemistry & Molecular Biology

Announcing the worldwide Protein Data Bank

H Berman et al.

NATURE STRUCTURAL BIOLOGY (2003)

Article Multidisciplinary Sciences

Antibody multispecificity mediated by conformational diversity

LC James et al.

SCIENCE (2003)

Article Biochemistry & Molecular Biology

Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field

E Krieger et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)

Article Biochemical Research Methods

Use of TLS parameters to model anisotropic displacements in macromolecular refinement

MD Winn et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2001)

Article Biochemical Research Methods

Rfree and the Rfree ratio.: II.: Calculation of the expected values and variances of cross-validation statistics in macromolecular least-squares refinement

IJ Tickle et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2000)