Principles for designing ideal protein structures (Q27675027)

6

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Nobuyasu Koga

object named as

Nobuyasu Koga

1

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David Baker

object named as

David Baker

7

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author name string

Rie Tatsumi-Koga

2

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Gaohua Liu

3

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Rong Xiao

4

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Thomas B Acton

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

5

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language of work or name

English

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publication date

8 November 2012

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published in

Nature

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volume

491

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issue

7423

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page(s)

222-7

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cites work

1 reference

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Potential of fragment recombination for rational design of proteins

20 March 2017

1 reference

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Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

20 March 2017

1 reference

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Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

20 March 2017

1 reference

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Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Predicting protein structures with a multiplayer online game

20 March 2017

1 reference

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

20 March 2017

1 reference

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TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet 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=3705962

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=3705962

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=3705962

Full-sequence computational design and solution structure of a thermostable protein variant

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

NMR data collection and analysis protocol for high-throughput protein structure determination

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Exploring steric constraints on protein mutations using MAGE/PROBE

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

High-resolution protein design with backbone freedom

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

De novo protein design: fully automated sequence selection

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Toward an outline of the topography of a realistic protein-folding funnel

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Protein folding funnels: a kinetic approach to the sequence-structure relationship

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

The program XEASY for computer-supported NMR spectral analysis of biological 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=3705962

Protein production by auto-induction in high density shaking cultures

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Refinement of protein structures in explicit solvent

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Torsion angle dynamics for NMR structure calculation with the new program DYANA

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

How to measure and predict the molar absorption coefficient of a protein

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

From Levinthal to pathways to funnels

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Recognition of errors in three-dimensional structures of proteins

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Assessment of protein models with three-dimensional profiles

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Evaluating protein structures determined by structural genomics consortia

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Protein structure prediction using Rosetta

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Dominant forces in protein folding

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

RosettaRemodel: a generalized framework for flexible backbone protein design.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Preparation of protein samples for NMR structure, function, and small-molecule screening studies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Theoretical and computational protein 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=3705962

Alternate states of proteins revealed by detailed energy landscape mapping

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Predicting peptide structures in native proteins from physical simulations of fragments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Computer-based design of novel protein structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

A topology-constrained distance network algorithm for protein structure determination from NOESY data.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

A structural alphabet for local protein structures: improved prediction methods

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

An integrated platform for automated analysis of protein NMR structures.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

De novo design of catalytic proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Computational design and characterization of a monomeric helical dinuclear metalloprotein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Contact order and ab initio protein structure prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

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=3705962

De novo design of helical bundles as models for understanding protein folding and function.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Prediction of local structure in proteins using a library of sequence-structure motifs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Theoretical Studies of Protein Folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

High-level production of uniformly ¹⁵N- and ¹³C-enriched fusion proteins in Escherichia coli.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3705962

Design of lambda Cro fold: solution structure of a monomeric variant of the de novo protein.

2 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE11600

Automated design of specificity in molecular recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE11600

Computational redesign of protein-protein interaction specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE11600

Physical-chemical determinants of turn conformations in globular proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE11600

Secondary structure determines protein topology

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE11600

Magnetic Field Dependence of Nitrogen−ProtonJSplittings in15N-Enriched Human Ubiquitin Resulting from Relaxation Interference and Residual Dipolar Coupling

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE11600

PROCHECK: a program to check the stereochemical quality of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE11600

Computational de novo design, and characterization of an A(2)B(2) diiron protein

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23135467

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein local structure prediction from sequence

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23135467

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NATURE11600

1 reference

Dimensions Publication ID

1043540416

0 references

1 reference

1 reference

PubMed publication ID

23135467

1 reference