Prediction and experimental validation of enzyme substrate specificity in protein structures (Q30557389)

19 August 2017

Prediction and experimental validation of enzyme substrate specificity in protein structures (English)

1 reference

protein structure prediction

19 August 2017

0 references

author

Serkan Erdin

series ordinal

2

1 reference

24 June 2017

5

Olivier Lichtarge

1 reference

19 August 2017

Shivas R Amin

1

1 reference

19 August 2017

R Matthew Ward

series ordinal

3

1 reference

19 August 2017

Rhonald C Lua

series ordinal

4

1 reference

19 August 2017

language of work or name

English

0 references

publication date

21 October 2013

1 reference

Proceedings of the National Academy of Sciences of the United States of America

19 August 2017

1 reference

19 August 2017

110

1 reference

19 August 2017

45

1 reference

19 August 2017

E4195-202

1 reference

PSC: protein surface classification

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

The use of evolutionary patterns in protein annotation

20 June 2018

1 reference

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COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

20 June 2018

1 reference

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Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding

20 June 2018

1 reference

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Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites

20 June 2018

1 reference

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Protein function prediction: towards integration of similarity metrics

20 June 2018

1 reference

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Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities

20 June 2018

1 reference

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SMpred: a support vector machine approach to identify structural motifs in protein structure without using evolutionary information

20 June 2018

1 reference

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Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification

20 June 2018

1 reference

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CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation

20 June 2018

1 reference

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Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors

20 June 2018

1 reference

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An angiotensin II type 1 receptor activation switch patch revealed through evolutionary trace analysis

20 June 2018

1 reference

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Evolutionary trace annotation of protein function in the structural proteome

20 June 2018

1 reference

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On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins

20 June 2018

1 reference

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The Universal Protein Resource (UniProt) in 2010

20 June 2018

1 reference

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Domain-ligand mapping for enzymes

20 June 2018

1 reference

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Structural relationships among proteins with different global topologies and their implications for function annotation strategies

20 June 2018

1 reference

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FLORA: a novel method to predict protein function from structure in diverse superfamilies

20 June 2018

1 reference

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FINDSITE: a threading-based approach to ligand homology modeling

20 June 2018

1 reference

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Protein function prediction--the power of multiplicity

20 June 2018

1 reference

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Protein function annotation by homology-based inference

20 June 2018

1 reference

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Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features

20 June 2018

1 reference

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Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Predicting protein function from sequence and structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Clustal W and Clustal X version 2.0

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Convergent algorithms for protein structural alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

What is the relationship between the global structures of apo and holo proteins?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Structure-based activity prediction for an enzyme of unknown function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

PAR-3D: a server to predict protein active site residues.

20 June 2018

1 reference

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MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor

20 June 2018

1 reference

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

20 June 2018

1 reference

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Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2

20 June 2018

1 reference

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

20 June 2018

1 reference

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PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt

20 June 2018

1 reference

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions

20 June 2018

1 reference

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Enzyme function less conserved than anticipated.

20 June 2018

1 reference

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Structural genomics: A pipeline for providing structures for the biologist

20 June 2018

1 reference

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The crystal structure of a hyper-thermophilic carboxylesterase from the archaeon Archaeoglobus fulgidus

20 June 2018

1 reference

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Prediction and confirmation of a site critical for effector regulation of RGS domain activity

20 June 2018

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A regulator of G protein signaling interaction surface linked to effector specificity

20 June 2018

1 reference

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Effects of noncatalytic residue mutations on substrate specificity and ligand binding of Thermobifida fusca endocellulase cel6A.

20 June 2018

1 reference

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20 June 2018

The Protein Data Bank

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Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily

20 June 2018

1 reference

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Computational analysis of chain flexibility and fluctuations in Rhizomucor miehei lipase.

20 June 2018

1 reference

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The role of proline and glycine in determining the backbone flexibility of a channel-forming peptide

20 June 2018

1 reference

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Overexpression and properties of a new thermophilic and thermostable esterase from Bacillus acidocaldarius with sequence similarity to hormone-sensitive lipase subfamily

20 June 2018

1 reference

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TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

20 June 2018

1 reference

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Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold

20 June 2018

1 reference

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

20 June 2018

1 reference

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Protein clefts in molecular recognition and function

20 June 2018

1 reference

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Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases

20 June 2018

1 reference

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Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex

20 June 2018

1 reference

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An evolutionary trace method defines binding surfaces common to protein families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Crystal structure of Escherichia coli QOR quinone oxidoreductase complexed with NADPH

20 June 2018

1 reference

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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

20 June 2018

1 reference

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The pathway of myo-inositol degradation in Aerobacter aerogenes. Dehydrogenation and dehydration

20 June 2018

1 reference

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Eye lens zeta-crystallin relationships to the family of "long-chain" alcohol/polyol dehydrogenases. Protein trimming and conservation of stable parts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

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

20 June 2018

1 reference

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Protein function prediction using local 3D templates

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Automated discovery of 3D motifs for protein function annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Genome-wide enzyme annotation with precision control: catalytic families (CatFam) databases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Identification of functional surfaces of the zinc binding domains of intracellular receptors

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Evolution of neural precursor selection: functional divergence of proneural proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Enantioselective analysis of ritalinic acids in biological samples by using a protein-based chiral stationary phase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Understanding the functional roles of amino acid residues in enzyme catalysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Structural and Sequence Comparisons of Quinone Oxidoreductase, ζ-Crystallin, and Glucose and Alcohol Dehydrogenases

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1305162110

Automated construction of structural motifs for predicting functional sites on protein structures.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3831482

Recombinant expression, purification, and characterization of three isoenzymes of aspartate aminotransferase from Arabidopsis thaliana

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24145433

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Practical limits of function prediction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24145433

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1305162110

1 reference

19 August 2017

0 references

1 reference

19 August 2017

1 reference