Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. (Q30357072)

16 September 2017

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. (English)

1 reference

16 September 2017

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0 references

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Mahendra D Chordia

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Heping Zheng

1 reference

16 September 2017

George M Sheldrick

1 reference

16 September 2017

David R Cooper

1 reference

16 September 2017

Peter Müller

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16 September 2017

19 December 2013

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16 September 2017

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16 September 2017

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16 September 2017

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16 September 2017

156-170

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Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank

16 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Visualizing ligand molecules in Twilight electron density

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

MetalPDB: a database of metal sites in biological macromolecular structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

High-resolution structure of Bombyx mori lipoprotein 7: crystallographic determination of the identity of the protein and its potential role in detoxification

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Structural and functional analysis of the archaeal endonuclease Nob1.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

REFMAC5 for the refinement of macromolecular crystal structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Unmet challenges of structural genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

How different oxidation states of crystalline myoglobin are influenced by X-rays

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Crystal Structure of the -Kinase Domain of Dictyostelium Myosin Heavy Chain Kinase A

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

PHENIX: a comprehensive Python-based system for macromolecular structure solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

MolProbity: all-atom structure validation for macromolecular crystallography

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Structural and functional characterization of plant aminoaldehyde dehydrogenase from Pisum sativum with a broad specificity for natural and synthetic aminoaldehydes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Copper binding to beta-2-microglobulin and its pre-amyloid oligomers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Recent developments in the methods and applications of the bond valence model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

ESG: extended similarity group method for automated protein function prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Biological X-ray absorption spectroscopy and metalloproteomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Trends in metal-binding and metalloprotein analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

MSDmotif: exploring protein sites and motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Data mining of metal ion environments present in protein structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

3 June 2018

A short history of SHELX

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Traditional biomolecular structure determination by NMR spectroscopy allows for major errors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

When X-rays modify the protein structure: radiation damage at work.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Coot: model-building tools for molecular graphics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Predicting metal-binding site residues in low-resolution structural models.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

The CCP4 suite: programs for protein crystallography

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

UCSF Chimera--a visualization system for exploratory research and analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

The structure of a universally employed enzyme: V8 protease from Staphylococcus aureus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

The Cambridge Structural Database: a quarter of a million crystal structures and rising

3 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

3 June 2018

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

3 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

PROMISE: a database of bioinorganic motifs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4410975

Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

3 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Expectation bias and information content

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Valence screening of water in protein crystals reveals potential Na+ binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Analysis of copper-ligand bond lengths in X-ray structures of different types of copper sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Jmol– a paradigm shift in crystallographic visualization

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Prediction of 3D metal binding sites from translated gene sequences based on remote-homology templates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Metal-MACiE: a database of metals involved in biological catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

The architecture of metal coordination groups in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Factors governing metal-ligand distances and coordination geometries of metal complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Nutrient regulates Tor1 nuclear localization and association with rDNA promoter.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Between objectivity and subjectivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Is the bond-valence method able to identify metal atoms in protein structures?

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Computational investigation of the histidine ammonia-lyase reaction: a modified loop conformation and the role of the zinc(II) ion

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

The assignment and validation of metal oxidation states in the Cambridge Structural Database

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

Structure of trypanothione reductase from Crithidia fasciculata at 2.6 A resolution; enzyme-NADP interactions at 2.8 A resolution

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2013.172

31 March 2020

1 reference

https://pubmed.ncbi.nlm.nih.gov/24356774

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NPROT.2013.172

1 reference

PMC publication ID

4410975

Dimensions Publication ID

16 September 2017

0 references

1 reference

PMC publication ID

4410975

16 September 2017

PubMed publication ID

24356774

1 reference

PMC publication ID

4410975