(Q34103089)

31 July 2017

title

Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase (English)

1 reference

31 July 2017

1 reference

5

Basuthkar J Rao

1 reference

31 July 2017

1

Sandeep Chakraborty

1 reference

31 July 2017

Renu Minda

2

1 reference

31 July 2017

Lipika Salaye

series ordinal

3

1 reference

31 July 2017

Swapan K Bhattacharjee

series ordinal

4

1 reference

31 July 2017

language of work or name

English

0 references

publication date

8 December 2011

1 reference

31 July 2017

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31 July 2017

volume

6

1 reference

31 July 2017

issue

12

1 reference

31 July 2017

page(s)

e28470

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

copyright license

start time

8 December 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Automated site preparation in physics-based rescoring of receptor ligand complexes

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

5 July 2018

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An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications

5 July 2018

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The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase

5 July 2018

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Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active-Site Metal Ion

5 July 2018

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Searching protein structure databases with DaliLite v.3

5 July 2018

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5 July 2018

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Very fast prediction and rationalization of pKa values for protein-ligand complexes

5 July 2018

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5 July 2018

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5 July 2018

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Functional and Structural Characterization of Four Glutaminases from Escherichia coli and Bacillus subtilis †

5 July 2018

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Alkaline Phosphatases : Structure, substrate specificity and functional relatedness to other members of a large superfamily of enzymes

5 July 2018

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5 July 2018

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Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications

5 July 2018

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Convergent evolution of enzyme active sites is not a rare phenomenon

5 July 2018

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Structure-based activity prediction for an enzyme of unknown function

5 July 2018

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5 July 2018

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5 July 2018

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Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction

5 July 2018

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The Acylation Mechanism of CTX-M β-Lactamase at 0.88 Å Resolution

5 July 2018

1 reference

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Crystal structure of alkaline phosphatase from the Antarctic bacterium TAB5

5 July 2018

1 reference

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Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

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5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Mimicking natural evolution in metallo-beta-lactamases through second-shell ligand mutations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

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5 July 2018

1 reference

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The importance of a critical protonation state and the fate of the catalytic steps in class A beta-lactamases and penicillin-binding proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

A new activity for an old enzyme: Escherichia coli bacterial alkaline phosphatase is a phosphite-dependent hydrogenase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Prediction of functional sites by analysis of sequence and structure conservation

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

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

5 July 2018

1 reference

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Calculating pKa values in enzyme active sites

5 July 2018

1 reference

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5 July 2018

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Structural basis for imipenem inhibition of class C beta-lactamases

5 July 2018

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5 July 2018

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Molecular dynamics simulations of biomolecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

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5 July 2018

1 reference

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The 1.9 A crystal structure of heat-labile shrimp alkaline phosphatase

5 July 2018

1 reference

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Structural basis of perturbed pKa values of catalytic groups in enzyme active sites

5 July 2018

1 reference

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An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

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

5 July 2018

1 reference

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5 July 2018

1 reference

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Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Crystal structure of alkaline phosphatase from human placenta at 1.8 A resolution. Implication for a substrate specificity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Structural and catalytic similarities between nucleotide pyrophosphatases/phosphodiesterases and alkaline phosphatases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

The Kyoto Encyclopedia of Genes and Genomes—KEGG

5 July 2018

1 reference

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A revised mechanism for the alkaline phosphatase reaction involving three metal ions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

EMBOSS: the European Molecular Biology Open Software Suite

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

The mechanism of the alkaline phosphatase reaction: insights from NMR, crystallography and site-specific mutagenesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Catalytic promiscuity and the evolution of new enzymatic activities

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

A superfamily of metalloenzymes unifies phosphopentomutase and cofactor-independent phosphoglycerate mutase with alkaline phosphatases and sulfatases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

pKa calculations for class A beta-lactamases: influence of substrate binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Recognition of spatial motifs in protein structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Catalytic properties of class A beta-lactamases: efficiency and diversity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

pKa calculations for class A beta-lactamases: methodological and mechanistic implications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

CATH--a hierarchic classification of protein domain structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Protein clefts in molecular recognition and function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Evolutionary families of peptidases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Classical electrostatics in biology and chemistry

5 July 2018

1 reference

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SCOP: a structural classification of proteins database for the investigation of sequences and structures

5 July 2018

1 reference

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pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

A database of protein structure families with common folding motifs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Enzyme recruitment in evolution of new function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

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

5 July 2018

1 reference

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The multiple common point set problem and its application to molecule binding pattern detection

21 January 2018

1 reference

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Evaluation of features for catalytic residue prediction in novel folds

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028470

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.PONE.0028470

Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028470

The unusual catalytic triad of poliovirus protease 3C.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028470

Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: a molecular dynamics simulation study

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028470

Sequence specific 1H, 13C and 15N backbone resonance assignments of UVI31+ from Chlamydomonas reinhardtii.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028470

BolA inhibits cell elongation and regulates MreB expression levels.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028470

Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Identifying structural motifs in proteins.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234256

Catalytic plasticity of fatty acid modification enzymes underlying chemical diversity of plant lipids

28 October 2018

1 reference

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Electrostatics in the active site of an alpha-amylase

28 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028470

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028470

Correlation between loss of alkaline phosphatase activity and accumulation of calcium during matrix vesicle-mediated mineralization

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22174814

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Converting trypsin to chymotrypsin: structural determinants of S1' specificity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22174814

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22174814

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0028470

1 reference

31 July 2017

0 references

1 reference

31 July 2017

1 reference