(Q28481742)

2

0 references

Z Nevin Gerek

3

0 references

M F Thorpe

4

0 references

S Banu Ozkan

PLOS Computational Biology

5

0 references

language of work or name

English

0 references

publication date

2012

0 references

published in

0 references

volume

8

0 references

issue

3

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page(s)

e1002428

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copyright license

Creative Commons CC0 License

start time

29 March 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

Enhancing the stability and solubility of the glucocorticoid receptor ligand-binding domain by high-throughput library screening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Analyzing protein structure and function using ancestral gene reconstruction

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

A method and server for predicting damaging missense mutations

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

De novo computational design of retro-aldol enzymes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Doubling the Size of the Glucocorticoid Receptor Ligand Binding Pocket by Deacylcortivazol

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Crystal structure of an ancient protein: evolution by conformational epistasis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Structure of human ferritin L chain

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Assessment of predictions submitted for the CASP6 comparative modeling category

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Resurrecting ancestral alcohol dehydrogenases from yeast

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

UCSF Chimera--a visualization system for exploratory research and analysis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

All-trans retinoic acid is a ligand for the orphan nuclear receptor ROR beta

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Catalytic promiscuity and the evolution of new enzymatic activities

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Relationship between sequence conservation and three-dimensional structure in a large family of esterases, lipases, and related proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Essential dynamics of proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

ProDy: protein dynamics inferred from theory and experiments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Allostery and population shift in drug discovery

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Messy biology and the origins of evolutionary innovations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Mutational effects and the evolution of new protein functions.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Union of geometric constraint-based simulations with molecular dynamics for 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=3315450

Mammalian Per-Arnt-Sim proteins in environmental adaptation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Stability effects of mutations and protein evolvability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Evaluation of CASP8 model quality predictions.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

In silico characterization of protein chimeras: relating sequence and function within the same fold.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

The sequence-structure relationship and protein function 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=3315450

Blind test of physics-based prediction of 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=3315450

SDR: a database of predicted specificity-determining residues in 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=3315450

Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

SNAP predicts effect of mutations on protein 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=3315450

Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Exploring the structure and function paradigm.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Protein folding by zipping and assembly

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Restriction of an extinct retrovirus by the human TRIM5alpha antiviral protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Analysis and prediction of functionally important sites in 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=3315450

Ancestral reconstruction of the ligand-binding pocket of Family C G protein-coupled receptors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Engineered antibody Fc variants with enhanced effector 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=3315450

Simulating protein evolution in sequence and structure space

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Protein dynamics and the immunological evolution of molecular recognition.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected 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=3315450

Computational design of receptor and sensor proteins with novel functions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

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=3315450

Mutation in the gene encoding ferritin light polypeptide causes dominant adult-onset basal ganglia disease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Evolution of function in protein superfamilies, from a structural perspective.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

CASP3 comparative modeling evaluation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3315450

Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002428

Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002428

Evolution of coral pigments recreated.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002428

Palaeotemperature trend for Precambrian life inferred from resurrected proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002428

Constrained geometric simulation of diffusive motion in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002428

Structural and biochemical mechanisms for the specificity of hormone binding and coactivator assembly by mineralocorticoid receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002428

Protein dynamics in a family of laboratory evolved thermophilic enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002428

Titration_DB: storage and analysis of NMR-monitored protein pH titration curves

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1002428

Probing the allosteric mechanism in pyrrolysyl-tRNA synthetase using energy-weighted network formalism

21 January 2018

1 reference

12 December 2020

Onset of cataract in early infancy associated with a 32G-->C transition in the iron responsive element of L-ferritin

1 reference

12 December 2020

Identifying protein folding cores from the evolution of flexible regions during unfolding

1 reference

12 December 2020

Conformational diversity and protein evolution--a 60-year-old hypothesis revisited

1 reference

12 December 2020

Analysis of ferritin genes in Parkinson disease

1 reference

12 December 2020

Do viral proteins possess unique biophysical features?

1 reference

12 December 2020

Generating stereochemically acceptable protein pathways

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1002428

Identifiers

DOI

0 references

DBLP publication ID

journals/ploscb/GlemboFGTO12

1 reference

DBLP Dataset 2021-01-02