Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis (Q27671312)

12

0 references

Farhad Forouhar

16

0 references

Gaetano T. Montelione

19

0 references

Kendall Houk

21

K N Houk

0 references

Zbigniew Pianowski

Zbigniew Pianowski

8

0 references

Liang Tong

Liang Tong

20

0 references

David Baker

David Baker

23

0 references

author name string

Florian Richter

1

0 references

Rebecca Blomberg

2

0 references

Sagar D Khare

3

0 references

Gert Kiss

4

0 references

Alexandre P Kuzin

5

0 references

Adam J T Smith

6

0 references

Jasmine Gallaher

7

0 references

Roger C Helgeson

9

0 references

Alexej Grjasnow

10

0 references

Rong Xiao

11

0 references

Min Su

13

0 references

Sergey Vorobiev

14

0 references

Scott Lew

15

0 references

Gregory J Kornhaber

17

0 references

John F Hunt

18

0 references

Donald Hilvert

Journal of the American Chemical Society

22

0 references

language of work or name

English

0 references

publication date

3 October 2012

0 references

published in

0 references

volume

134

0 references

issue

39

0 references

page(s)

16197-206

0 references

cites work

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Kemp elimination catalysts by computational enzyme design

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

De novo computational design of retro-aldol enzymes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Specific recognition of saturated and 4,5-unsaturated hexuronate sugars by a periplasmic binding protein involved in pectin catabolism

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Site-directed mutagenesis and the role of the oxyanion hole in subtilisin

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Dipeptidyl peptidase IV and related enzymes in cell biology and liver disorders

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

De Novo Enzyme Design Using Rosetta3

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Cytosolic phospholipase A2

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Serine protease mechanism and specificity

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Quantitative reactivity profiling predicts functional cysteines in proteomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Improved beta-lactam acylases and their use as industrial biocatalysts.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Trends and innovations in industrial biocatalysis for the production of fine chemicals.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Catalytic antibodies as designer proteases and esterases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Enzyme-like proteins by computational 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=4104585

Hydrolytic antibodies: variations on a theme

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Plasminogen activators and matrix metalloproteinases in angiogenesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Exploring the active site of chorismate mutase by combinatorial mutagenesis and selection: the importance of electrostatic catalysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Site-directed mutagenesis of a catalytic antibody: an arginine and a histidine residue play key roles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

A genetic approach to the generation of antibodies with enhanced catalytic activities

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Dissection of an antibody-catalyzed reaction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Evaluation and ranking of enzyme designs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

New algorithms and an in silico benchmark for computational enzyme design

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

PAPAIN-CATALYSED HYDROLYSIS OF SOME HIPPURIC ESTERS. A NEW MECHANISM FOR PAPAIN-CATALYSED HYDROLYSIS.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Theozymes and compuzymes: theoretical models for biological catalysis

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Proteases and Protease Inhibitors in Tumor Progression

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Evidence that the lack of high catalytic activity of thiolsubtilisin towards specific substrates may be due to an inappropriately located proton-distribution system. Demonstration of highly nucleophilic character of the thiol group of thiolsubtilisi

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Demonstration of a change in the rate-determining step in papain- and ficin-catalyzed acyl-transfer reactions

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Induction of an Antibody That Catalyzes the Hydrolysis of an Amide Bond

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Dissecting the catalytic triad of a serine protease

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

RosettaLigand docking with full ligand and receptor flexibility

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Quantum mechanical design of enzyme active sites

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Multiple active site corrections for docking and virtual screening.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4104585

Probing the mechanism and improving the rate of substrate-assisted catalysis in subtilisin BPN'

27 November 2018

1 reference

12 December 2020

Assessing the performance of OMEGA with respect to retrieving bioactive conformations

1 reference

12 December 2020

Tour de paclitaxel: biocatalysis for semisynthesis

1 reference

12 December 2020

The catalytic role of the active site aspartic acid in serine proteases

1 reference

12 December 2020

Structural and Functional Roles of Asparagine 175 in the Cysteine Protease Papain

1 reference

12 December 2020

Biomimetic Reactions Catalyzed by Cyclodextrins and Their Derivatives

1 reference

12 December 2020

Cysteine Proteases and Their Inhibitors

1 reference

12 December 2020

The Design of Molecular Hosts, Guests, and Their Complexes (Nobel Lecture)

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1021/JA3037367

On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models

1 reference

9 October 2024

https://opencitations.net/index/api/v1/references/10.1021/JA3037367

Identifiers

DOI

10.1021/JA3037367

1 reference

1 reference

1 reference

PubMed publication ID

22871159

1 reference