Computational protein design with explicit consideration of surface hydrophobic patches (Q41039615)

25 September 2017

Computational protein design with explicit consideration of surface hydrophobic patches (English)

1 reference

25 September 2017

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computational biology

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Brian Kuhlman

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25 September 2017

Andrew Leaver-Fay

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25 September 2017

Ron Jacak

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PMC publication ID

3277657

25 September 2017

language of work or name

English

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publication date

16 December 2011

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25 September 2017

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25 September 2017

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25 September 2017

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25 September 2017

825-838

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

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Design of therapeutic proteins with enhanced stability.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Evaluating and optimizing computational protein design force fields using fixed composition-based negative design

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Modeling backbone flexibility improves protein stability estimation.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Inference of macromolecular assemblies from crystalline state

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Supercharging proteins can impart unusual resilience

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Protein structure prediction using Rosetta

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

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

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Rationalization of the effects of mutations on peptide and protein aggregation rates.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

PISCES: a protein sequence culling server

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Folding free energy function selects native-like protein sequences in the core but not on the surface

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Native protein sequences are close to optimal for their structures

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Automatic protein design with all atom force-fields by exact and heuristic optimization

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

26 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

De novo protein design. I. In search of stability and specificity.

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Effective energy function for proteins in solution

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

De novo protein design: towards fully automated sequence selection

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Probing the role of packing specificity in protein design

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Bayesian statistical analysis of protein side‐chain rotamer preferences

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Principles of protein-protein interactions

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

The nature of the accessible and buried surfaces in proteins

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Automated design of the surface positions of protein helices

26 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Designing amino acid sequences to fold with good hydrophobic cores

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Maintaining solvent accessible surface area under rotamer substitution for protein design.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Automated design of specificity in molecular recognition

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

An improved equivalence algorithm

19 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.23241

Stability and function: two constraints in the evolution of barstar and other proteins

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277657

Surface, subunit interfaces and interior of oligomeric proteins

4 November 2018

1 reference

12 December 2020

Surface-exposed phenylalanines in the RNP1/RNP2 motif stabilize the cold-shock protein CspB from Bacillus subtilis

1 reference

12 December 2020

Modeling unfolded states of peptides and proteins

1 reference

12 December 2020

Computational Protein Design Using Flexible Backbone Remodeling and Resurfacing: Case Studies in Structure-Based Antigen Design

1 reference

12 December 2020

Progressive stabilization of intermediate and transition states in protein folding reactions by introducing surface hydrophobic residues

1 reference

12 December 2020

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

1 reference

12 December 2020

A method for detecting hydrophobic patches on protein surfaces

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.23241

1 reference

25 September 2017

1 reference

PMC publication ID

3277657

25 September 2017

PubMed publication ID

22223219

1 reference

PMC publication ID

3277657