(Q28472023)

2

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author name string

John A Capra

1

0 references

Mona Singh

4

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Thomas A Funkhouser

PLOS Computational Biology

5

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language of work or name

English

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publication date

December 2009

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published in

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volume

5

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issue

12

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page(s)

e1000585

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copyright license

Creative Commons Attribution 4.0 International

start time

4 December 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA

1 reference

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Protein-protein interaction hotspots carved into sequences

19 March 2017

1 reference

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CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

19 March 2017

1 reference

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Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design

19 March 2017

1 reference

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Sequence variation in ligand binding sites in proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

SITEHOUND-web: a server for ligand binding site identification in protein structures.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Robust recognition of zinc binding sites in proteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

LigASite--a database of biologically relevant binding sites in proteins with known apo-structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

PocketPicker: analysis of ligand binding-sites with shape descriptors.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Functional specificity lies within the properties and evolutionary changes of amino acids

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Interaction-site prediction for protein complexes: a critical assessment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

firestar--prediction of functionally important residues using structural templates and alignment reliability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Incorporating background frequency improves entropy-based residue conservation measures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

ET viewer: an application for predicting and visualizing functional sites in protein structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

On the nature of cavities on protein surfaces: application to the identification of drug-binding sites

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Pocketome via comprehensive identification and classification of ligand binding envelopes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

A family of evolution-entropy hybrid methods for ranking protein residues by importance.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Prediction of functional sites by analysis of sequence and structure conservation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

SiteLight: binding-site prediction using phage display libraries

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Scoring residue conservation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Prediction of functionally important residues based solely on the computed energetics of protein structure.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

The HSSP database of protein structure-sequence alignments and family profiles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Characterization and prediction of residues determining protein functional specificity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Clustering protein environments for function prediction: finding PROSITE motifs in 3D

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Protein clefts in molecular recognition and function

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2777313

Predicting functionally important residues from sequence conservation

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Evaluation of features for catalytic residue prediction in novel folds

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Analysis and prediction of functional sub-types from protein sequence alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Fast prediction and visualization of protein binding pockets with PASS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Improving position-specific predictions of protein functional sites using phylogenetic motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Prediction of protein functional residues from sequence by probability density estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Detection of functionally important regions in "hypothetical proteins" of known structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Distinguishing structural and functional restraints in evolution in order to identify interaction sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Using a neural network and spatial clustering to predict the location of active sites in enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Predicting small ligand binding sites in proteins using backbone structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

A method for localizing ligand binding pockets in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

PQS: a protein quaternary structure file server

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Side-chain flexibility in proteins upon ligand binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Analysis of catalytic residues in enzyme active sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Network Analysis of Protein Structures Identifies Functional Residues

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000585

Automatic methods for predicting functionally important residues

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19997483

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000585

1 reference

journals/ploscb/CapraLTSF09

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

PubMed publication ID

19997483

1 reference