Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design (Q34198887)

31 July 2017

title

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design (English)

1 reference

31 July 2017

0 references

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David Baker

2

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author name string

Summer B Thyme

series ordinal

1

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31 July 2017

Philip Bradley

series ordinal

3

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31 July 2017

language of work or name

English

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publication date

15 March 2012

1 reference

Journal of Molecular Biology

31 July 2017

published in

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31 July 2017

volume

419

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31 July 2017

issue

3-4

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31 July 2017

page(s)

255-274

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Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design

31 July 2017

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display

5 July 2018

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Motif-directed flexible backbone design of functional interactions

5 July 2018

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Alteration of enzyme specificity by computational loop remodeling and design

5 July 2018

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Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface

5 July 2018

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Assessment of the optimization of affinity and specificity at protein-DNA interfaces

5 July 2018

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Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation

5 July 2018

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Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases

5 July 2018

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

5 July 2018

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Kemp elimination catalysts by computational enzyme design

5 July 2018

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Coevolution of a Homing Endonuclease and Its Host Target Sequence

5 July 2018

1 reference

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Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution

5 July 2018

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Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL.

5 July 2018

1 reference

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5 July 2018

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Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

5 July 2018

1 reference

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Computational redesign of endonuclease DNA binding and cleavage specificity

5 July 2018

1 reference

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Directed evolution and substrate specificity profile of homing endonuclease I-SceI.

5 July 2018

1 reference

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In vivo selection of engineered homing endonucleases using double-strand break induced homologous recombination

5 July 2018

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Protein-DNA binding specificity predictions with structural models

5 July 2018

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A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces

5 July 2018

1 reference

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Design, activity, and structure of a highly specific artificial endonuclease

5 July 2018

1 reference

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Computational method to reduce the search space for directed protein evolution

5 July 2018

1 reference

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5 July 2018

The Protein Data Bank

1 reference

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Effective energy function for proteins in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

Structure-based prediction of DNA target sites by regulatory proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

Bayesian statistical analysis of protein side-chain rotamer preferences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

Protein-DNA interaction. No code for recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

Basic local alignment search tool

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

Modular structure of transcription factors: implications for gene regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

Latent evolutionary potentials under the neutral mutational drift of an enzyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

A simple physical model for the prediction and design of protein-DNA interactions

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

DNA sequence and structure: direct and indirect recognition in protein-DNA binding

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3566986

Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22426128

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.JMB.2012.03.005

1 reference

31 July 2017

1 reference

31 July 2017

1 reference