Computational structure-based redesign of enzyme activity (Q34948584)

5 August 2017

title

Computational structure-based redesign of enzyme activity (English)

1 reference

Correction for Chen et al., Computational structure-based redesign of enzyme activity

5 August 2017

corrigendum / erratum

0 references

2

Ivelin Georgiev

1 reference

5 August 2017

Cheng-Yu Chen

1

1 reference

5 August 2017

Amy C Anderson

series ordinal

3

1 reference

5 August 2017

Bruce R Donald

series ordinal

4

1 reference

5 August 2017

language of work or name

English

0 references

publication date

19 February 2009

1 reference

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

5 August 2017

published in

1 reference

5 August 2017

volume

106

1 reference

5 August 2017

issue

10

1 reference

5 August 2017

page(s)

3764-3769

1 reference

The dead-end elimination theorem and its use in protein side-chain positioning

5 August 2017

cites work

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

8 July 2018

https://api.crossref.org/works/10.1073%2FPNAS.0900266106

Algorithm for backrub motions in protein design

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

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=2645347

De novo computational design of retro-aldol 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=2645347

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Computational design of antibody-affinity improvement beyond in vivo maturation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Dead-end elimination with backbone flexibility

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Directed evolution can rapidly improve the activity of chimeric assembly-line 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=2645347

Electrostatics in computational protein 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=2645347

Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational 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=2645347

Computational thermostabilization of an enzyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Learning from nature's drug factories: nonribosomal synthesis of macrocyclic peptides

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Computational design of receptor and sensor proteins with novel functions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Exploitation of the selectivity-conferring code of nonribosomal peptide synthetases for the rational design of novel peptide antibiotics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Enzyme-like proteins by computational 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=2645347

Computational method to reduce the search space for directed protein evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

The penultimate rotamer library

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Energy functions for protein 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=2645347

The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Effective energy function for proteins 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=2645347

Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Directed evolution of enzyme catalysts

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

De novo protein design: fully automated sequence selection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Redesigning the PheA domain of gramicidin synthetase leads to a new understanding of the enzyme's mechanism and selectivity.

8 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0900266106

Improving catalytic function by ProSAR-driven enzyme evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0900266106

A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0900266106

Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0900266106

Substrate recognition and selection by the initiation module PheATE of gramicidin S synthetase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0900266106

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0900266106

Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645347

Purification and properties of gentamicin nucleotidyltransferase from Escherichia coli: Nucleotide specificity, pH optimum, and the separation of two electrophoretic variants

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19228942

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0900266106

1 reference

5 August 2017

0 references

1 reference

5 August 2017

1 reference