The PDB_REDO server for macromolecular structure model optimization (Q35215523)

7 August 2017

The PDB_REDO server for macromolecular structure model optimization (English)

1 reference

7 August 2017

macromolecular structure

0 references

1 reference

4

1 reference

7 August 2017

Robbie P Joosten

1

0 references

author name string

Fei Long

series ordinal

2

1 reference

PubMed ID

25075342

7 August 2017

Garib N Murshudov

series ordinal

3

1 reference

7 August 2017

30 May 2014

1 reference

7 August 2017

1 reference

7 August 2017

1

1 reference

7 August 2017

Pt 4

1 reference

7 August 2017

213-220

1 reference

Processing of X-ray diffraction data collected in oscillation mode

7 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

28 July 2018

Decision making in xia2.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

A new generation of crystallographic validation tools for the protein data bank

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

REFMAC5 for the refinement of macromolecular crystal structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Recent advances in the CRANK software suite for experimental phasing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Data processing and analysis with the autoPROC toolbox

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Features and development of Coot

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Phasercrystallographic software

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

BALBES: a molecular-replacement pipeline

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

The Buccaneer software for automated model building. 1. Tracing protein chains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Coot: model-building tools for molecular graphics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

APRV - a program for automated data processing, refinement and visualization.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Refinement of macromolecular structures by the maximum-likelihood method

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

From The Cover: Automated protein crystal structure determination using ELVES

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Stereochemistry of polypeptide chain configurations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Automated crystallographic system for high-throughput protein structure determination.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Automated protein model building combined with iterative structure refinement

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Objectively judging the quality of a protein structure from a Ramachandran plot

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Errors in protein structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

The Protein Data Bank: a computer-based archival file for macromolecular structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Linking Crystallographic Model and Data Quality

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

PDB_REDO: constructive validation, more than just looking for errors

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Statistical quality indicators for electron-density maps

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Overview of the CCP4 suite and current developments

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Automated search-model discovery and preparation for structure solution by molecular replacement.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

Checking your imagination: applications of the free R value

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4107921

The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites

26 September 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514009324

PDB Improvement Starts with Data Deposition

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514009324

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514009324

XDSAPP: a graphical user interface for the convenient processing of diffraction data usingXDS

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514009324

Between objectivity and subjectivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1107%2FS2052252514009324

Automatic modeling of protein backbones in electron-density maps via prediction of Calpha coordinates

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25075342

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25075342

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The use of position-specific rotamers in model building by homology

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25075342

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1107/S2052252514009324

1 reference

7 August 2017

1 reference

7 August 2017

1 reference

PubMed ID

25075342