(Q34694427)

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

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scholarly article

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Europe PubMed Central

PubMed publication ID

4 August 2017

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

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Europe PubMed Central

PubMed publication ID

4 August 2017

machine learning

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Michal Brylinski

1

object named as

Michal Brylinski

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

Jeffrey Skolnick

2

object named as

Jeffrey Skolnick

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Europe PubMed Central

PubMed publication ID

4 August 2017

language of work or name

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publication date

6 December 2010

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Europe PubMed Central

PubMed publication ID

4 August 2017

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Europe PubMed Central

PubMed publication ID

4 August 2017

79

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Europe PubMed Central

PubMed publication ID

4 August 2017

3

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

735-751

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Evolutionary trace annotation of protein function in the structural proteome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Metalloproteomes: a bioinformatic approach.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Function and biogenesis of iron-sulphur proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Bacterial genome sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Template-free protein structure prediction and quality assessment with an all-atom free-energy model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

FINDSITE: a combined evolution/structure-based approach to protein function prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Protein function annotation by homology-based inference

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Sequence-based feature prediction and annotation of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Protein structure prediction and model quality assessment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Protein-folding location can regulate manganese-binding versus copper- or zinc-binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

I-TASSER server for protein 3D structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Preservation of protein clefts in comparative models.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Fast procedure for reconstruction of full-atom protein models from reduced representations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Robust recognition of zinc binding sites in proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Assessment of CASP7 predictions for template-based modeling targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Ab initio protein structure prediction using chunk-TASSER

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Discovering structural motifs using a structural alphabet: application to magnesium-binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Predicting zinc binding at the proteome level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Automated protein function prediction--the genomic challenge

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

The PROSITE database.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Progress over the first decade of CASP experiments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Functional annotation by identification of local surface similarities: a novel tool for structural genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Progress of structural genomics initiatives: an analysis of solved target structures.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

TM-align: a protein structure alignment algorithm based on the TM-score

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

The Universal Protein Resource (UniProt)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Structural insights into protein-metal ion partnerships.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Scoring function for automated assessment of protein structure template quality

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Automated structure prediction of weakly homologous proteins on a genomic scale

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Prediction of protein function from protein sequence and structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Identifying protein function--a call for community action

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Automatic prediction of protein function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

PISCES: a protein sequence culling server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Function first: a powerful approach to post-genomic drug discovery

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Structural and Functional Aspects of Metal Sites in Biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

The Ensembl genome database project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Extending the accuracy limits of prediction for side-chain conformations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Geometry of metal-ligand interactions in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Defrosting the frozen approximation: PROSPECTOR--a new approach to threading.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

MaxSub: an automated measure for the assessment of protein structure prediction quality.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Comparative protein structure modeling of genes and genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Zinc-dependent protein folding

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 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=3060289

7 July 2018

Are predicted structures good enough to preserve functional sites?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Automated analysis of interatomic contacts in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Twilight zone of protein sequence alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Advances in comparative protein-structure modelling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Functional non-heme iron metalloenzyme model systems.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Metalloenzymes, structural motifs, and inorganic models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Metal protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Where metal ions bind in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3060289

7 July 2018

How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

In silico identification of putative metal binding motifs.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

The architecture of metal coordination groups in proteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Comparison of structure-based and threading-based approaches to protein functional annotation

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

The prediction and characterization of metal binding sites in proteins.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Molecular modeling of protein function regions.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

A solution for the best rotation to relate two sets of vectors

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

A scoring function for docking ligands to low-resolution protein structures.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

A Mathematical Theory of Communication

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Bayesian Network Classifiers

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

TASSER: an automated method for the prediction of protein tertiary structures in CASP6.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Prediction of zinc-binding sites in proteins from sequence.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Occurrence of copper proteins through the three domains of life: a bioinformatic approach

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Non-heme iron through the three domains of life

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22913

21 January 2018

Metalloproteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/21287609

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Exploiting 3D structural templates for detection of metal-binding sites in protein structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/21287609

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1002/PROT.22913

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

ResearchGate publication ID

0 references

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