Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination (Q37187139)

18 August 2017

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination (English)

1 reference

18 August 2017

Daniela Röthlisberger

2

Daniela Röthlisberger

0 references

David Baker

David Baker

3

0 references

William L. Jorgensen

4

William L Jorgensen

1 reference

18 August 2017

Anastassia N. Alexandrova

1

Anastassia N Alexandrova

1 reference

18 August 2017

language of work or name

English

0 references

publication date

1 November 2008

1 reference

Journal of the American Chemical Society

18 August 2017

1 reference

18 August 2017

130

1 reference

18 August 2017

47

1 reference

18 August 2017

15907-15915

1 reference

Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Kemp elimination catalysts by computational enzyme design

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

De novo computational design of retro-aldol enzymes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Protein design: reengineering cellular retinoic acid binding protein II into a rhodopsin protein mimic

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Why urea eliminates ammonia rather than hydrolyzes in aqueous solution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Electrostatic basis for enzyme catalysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Mechanisms and free energies of enzymatic reactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

De novo design of catalytic proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Computational design of a Zn2+receptor that controls bacterial gene expression

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

The catalytic mechanism of indole-3-glycerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Enzyme-like proteins by computational design

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Critical analysis of antibody catalysis.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Construction of a catalytically active iron superoxide dismutase by rational protein design

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Protein design automation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

New algorithms and an in silico benchmark for computational enzyme design

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

At the crossroads of chemistry and immunology: catalytic antibodies

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Macrophomate synthase: QM/MM simulations address the Diels-Alder versus Michael-Aldol reaction mechanism

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Steric retardation of SN2 reactions in the gas phase and solution

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Accuracy of free energies of hydration using CM1 and CM3 atomic charges

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Investigation of solvent effects for the Claisen rearrangement of chorismate to prephenate: mechanistic interpretation via near attack conformations

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2680199

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

4 December 2018

1 reference

12 December 2020

Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations

1 reference

12 December 2020

Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens

1 reference

12 December 2020

Cope elimination: elucidation of solvent effects from QM/MM simulations

1 reference

12 December 2020

Comparison of simple potential functions for simulating liquid water

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1021/JA804040S

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1021/JA804040S

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

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1021/JA804040S

Identifiers

DOI

10.1021/JA804040S

1 reference

18 August 2017

1 reference

18 August 2017

PubMed publication ID

18975945

1 reference