Predicting Nonspecific Ion Binding Using DelPhi (Q36047365)

11 August 2017

Predicting nonspecific ion binding using DelPhi (English)

1 reference

11 August 2017

Predicting Nonspecific Ion Binding Using DelPhi (English)

1 reference

https://api.crossref.org/works/10.1016/J.BPJ.2012.05.013

5 January 2025

main subject

computational biology

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A22735539

5 January 2025

author name string

Marharyta Petukh

1

1 reference

11 August 2017

Maxim Zhenirovskyy

2

1 reference

11 August 2017

Chuan Li

3

1 reference

11 August 2017

Lin Li

4

1 reference

11 August 2017

Lin Wang

5

1 reference

11 August 2017

Emil Alexov

6

1 reference

11 August 2017

language of work or name

English

0 references

publication date

19 June 2012

1 reference

full work available at URL

11 August 2017

http://www.cell.com/article/S0006349512005668/pdf

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A22735539

https://europepmc.org/articles/PMC3379622

5 January 2025

file format

HyperText Markup Language

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A22735539

https://europepmc.org/articles/PMC3379622?pdf=render

5 January 2025

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A22735539

https://doi.org/10.1016/j.bpj.2012.05.013

5 January 2025

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A22735539

https://api.elsevier.com/content/article/PII:S0006349512005668?httpAccept=text/xml

5 January 2025

1 reference

https://api.crossref.org/works/10.1016/J.BPJ.2012.05.013

https://api.elsevier.com/content/article/PII:S0006349512005668?httpAccept=text/plain

5 January 2025

1 reference

https://api.crossref.org/works/10.1016/J.BPJ.2012.05.013

5 January 2025

1 reference

11 August 2017

102

1 reference

11 August 2017

12

1 reference

11 August 2017

2885-2893

1 reference

Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born Models

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

A strategy for reducing gross errors in the generalized Born models of implicit solvation.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Crystal structure of HLA-DP2 and implications for chronic beryllium disease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Prediction of transition metal-binding sites from apo protein structures.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Prediction of water and metal binding sites and their affinities by using the Fold-X force field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Protein metal binding residue prediction based on neural networks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Redox active calcium ion channels and cell death

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Development and testing of a general amber force field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

The role of dietary calcium in bone health

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Effective Born radii in the generalized Born approximation: the importance of being perfect

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Metal ions in the structure and function of RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Geometry of metal-ligand interactions in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

2 October 2017

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=3379622

Neuronal Calcium Signaling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

The extended environment of mononuclear metal centers in protein structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Magnesium metabolism: a review

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

The interpretation of protein structures: Estimation of static accessibility

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Geometry of interaction of metal ions with sulfur-containing ligands in protein structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Where metal ions bind in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Zinc coordination, function, and structure of zinc enzymes and other proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Structural Aspects of Metal Liganding to Functional Groups in Proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Analysis of zinc binding sites in protein crystal structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Geometry of interaction of metal ions with histidine residues in protein structures

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Interaction of metal ions with carboxylic and carboxamide groups in protein structures

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Physical basis of structural and catalytic Zn-binding sites in proteins

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Macroscopic electrostatic models for protonation states in proteins

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

A hint to search for metalloproteins in gene banks

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Stabilization of secondary structure of Alzheimer beta-protein by aluminum(III) ions and D-Asp substitutions

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3379622

Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22735539

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22735539

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22735539

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Metal ions

6

1 reference

https://api.crossref.org/works/10.1016/J.BPJ.2012.05.013

Semianalytical treatment of solvation for molecular mechanics and dynamics

5 January 2025

44

1 reference

https://api.crossref.org/works/10.1016/J.BPJ.2012.05.013

5 January 2025

Identifiers

1 reference

11 August 2017

1 reference

11 August 2017

1 reference