(Q33706085)

28 July 2017

Toward accurate screening in computer-aided enzyme design (English)

1 reference

Alexandra Vardi-Kilshtain

28 July 2017

series ordinal

2

object named as

Alexandra Vardi-Kilshtain

1 reference

28 July 2017

3

Arieh Warshel

1 reference

28 July 2017

1

Maite Roca

1 reference

PubMed ID

19161327

28 July 2017

language of work or name

English

0 references

publication date

1 April 2009

1 reference

28 July 2017

1 reference

28 July 2017

48

1 reference

28 July 2017

3046-3056

1 reference

28 July 2017

14

1 reference

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies

28 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

On the relationship between folding and chemical landscapes in enzyme catalysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Kemp elimination catalysts by computational enzyme design

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

De novo computational design of retro-aldol enzymes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

On the relationship between thermal stability and catalytic power of enzymes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Structure and dynamics of a molten globular enzyme

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Selection and evolution of enzymes from a partially randomized non-catalytic scaffold

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Progress in computational protein design

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Minimalist active-site redesign: teaching old enzymes new tricks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Modeling electrostatic effects in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Electrostatic basis for enzyme catalysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Knowledge-based potentials in protein design.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

An enzymatic molten globule: efficient coupling of folding and catalysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

De novo design of catalytic proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Mixed quantum mechanical/molecular mechanical (QM/MM) study of the deacylation reaction in a penicillin binding protein (PBP) versus in a class C beta-lactamase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Enzyme-like proteins by computational design

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

What are the dielectric "constants" of proteins and how to validate electrostatic models?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

A strategically positioned cation is crucial for efficient catalysis by chorismate mutase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

The monofunctional chorismate mutase from Bacillus subtilis. Structure determination of chorismate mutase and its complexes with a transition state analog and prephenate, and implications for the mechanism of the enzymatic reaction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Toward computer-aided site-directed mutagenesis of enzymes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Bicycle-pedal model for the first step in the vision process

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Relative tolerance of an enzymatic molten globule and its thermostable counterpart to point mutation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Predicting drug-resistant mutations of HIV protease

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Exhaustive mutagenesis of six secondary active-site residues in Escherichia coli chorismate mutase shows the importance of hydrophobic side chains and a helix N-capping position for stability and catalysis

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Electrostatic contributions to protein stability and folding energy

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

On the generation of catalytic antibodies by transition state analogues.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Electrostatic contributions to protein-protein binding affinities: application to Rap/Raf interaction

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832760

Semiquantitative calculations of catalytic free energies in genetically modified enzymes

30 October 2018

1 reference

12 December 2020

Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin

1 reference

12 December 2020

Energetics of nucleophile activation in a protein tyrosine phosphatase

1 reference

12 December 2020

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

1 reference

12 December 2020

Computational enzymology: modelling the mechanisms of biological catalysts

1 reference

12 December 2020

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/BI802191B

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/BI802191B

Identifiers

DOI

10.1021/BI802191B

1 reference

release_eos6abei6jc4xnv7s45b7j6cl4

28 July 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/eos6abei6jc4xnv7s45b7j6cl4

24 November 2022

mapped directly with Wikidata item

PMCID

2832760

1 reference

28 July 2017

1 reference

PubMed ID

19161327