(Q34917956)

5 August 2017

Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis (English)

1 reference

5 August 2017

3

Arieh Warshel

1 reference

5 August 2017

1

Maria P Frushicheva

1 reference

5 August 2017

Jie Cao

2

1 reference

PubMed ID

21443179

5 August 2017

language of work or name

English

0 references

publication date

15 April 2011

1 reference

5 August 2017

10

1 reference

inferred from page(s)

published in

Biochemistry

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5 August 2017

50

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5 August 2017

3849-3858

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5 August 2017

18

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The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions

5 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Conformational diversity and computational enzyme design

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

An exciting but challenging road ahead for computational enzyme design

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Evaluation and ranking of enzyme designs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Role of water in the multifaceted catalytic antibody 4B2 for allylic isomerization and Kemp elimination reactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Effective approach for calculations of absolute stability of proteins using focused dielectric constants

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

A 21st century revisionist's view at a turning point in enzymology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

On unjustifiably misrepresenting the EVB approach while simultaneously adopting it

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Toward accurate screening in computer-aided enzyme design

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Kemp elimination catalysts by computational enzyme design

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

A new drug binding subsite on human serum albumin and drug-drug interaction studied by X-ray crystallography

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Minimalist active-site redesign: teaching old enzymes new tricks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Electrostatic basis for enzyme catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Structural origins of efficient proton abstraction from carbon by a catalytic antibody

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Nonspecific medium effects versus specific group positioning in the antibody and albumin catalysis of the base-promoted ring-opening reactions of benzisoxazoles

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Why does the Ras switch "break" by oncogenic mutations?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Toward computer-aided site-directed mutagenesis of enzymes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

On the energetics of ATP hydrolysis in solution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Dineopentyl phosphate hydrolysis: evidence for stepwise water attack

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Predicting an improvement of secondary catalytic activity of promiscuous isochorismate pyruvate lyase by computational design.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Large rate accelerations in antibody catalysis by strategic use of haptenic charge

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3086991

Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations

26 October 2018

1 reference

12 December 2020

On the magnitude and specificity of medium effects in enzyme-like catalysts for proton transfer

1 reference

12 December 2020

Computational enzymology: modelling the mechanisms of biological catalysts

1 reference

12 December 2020

Computer-aided rational design of catalytic antibodies: The 1F7 case

1 reference

12 December 2020

Semiquantitative calculations of catalytic free energies in genetically modified enzymes

1 reference

12 December 2020

What about protein polarity?

1 reference

12 December 2020

Physical organic chemistry of benzisoxazoles. II. Linearity of the Broensted free energy relation for the base-catalyzed decomposition of benzisoxazoles

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/BI200063A

Enhancing activity and controlling stereoselectivity in a designed PLP-dependent aldolase.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/BI200063A

Identifiers

DOI

10.1021/BI200063A

1 reference

5 August 2017

1 reference

5 August 2017

1 reference

PubMed ID

21443179