Structural and dynamic determinants of protein-peptide recognition (Q30423438)

15 September 2017

Structural and dynamic determinants of protein-peptide recognition (English)

1 reference

15 September 2017

4

1 reference

15 September 2017

5

1 reference

15 September 2017

Elizabeth A Proctor

2

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Onur Dagliyan

object named as

Onur Dagliyan

series ordinal

1

0 references

author name string

Kevin M D'Auria

series ordinal

3

1 reference

15 September 2017

1 December 2011

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15 September 2017

1 reference

15 September 2017

19

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15 September 2017

1837-1845

1 reference

15 September 2017

12

1 reference

How does a drug molecule find its target binding site?

15 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Rapid flexible docking using a stochastic rotamer library of ligands

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Engineered allosteric activation of kinases in living cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Protein pockets: inventory, shape, and comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

The structural basis of peptide-protein binding strategies.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Synthetic therapeutic peptides: science and market

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Computational design of affinity and specificity at protein-protein interfaces

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Structural basis for proteolytic specificity of the human apoptosis-inducing granzyme M

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Accurate prediction of peptide binding sites on protein surfaces.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

MedusaScore: an accurate force field-based scoring function for virtual drug screening

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Ab initio folding of proteins with all-atom discrete molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

firestar--prediction of functionally important residues using structural templates and alignment reliability

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Visualization of transient encounter complexes in protein-protein association.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Systematic discovery of new recognition peptides mediating protein interaction networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

The role of electrostatic interactions in calmodulin-peptide complex formation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Protein structure and enzyme action.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Efficient docking of peptides to proteins without prior knowledge of the binding site

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

The free energy landscape for beta hairpin folding in explicit water

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Electrostatic aspects of protein-protein interactions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Accommodating protein flexibility in computational drug design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Effective energy function for proteins in solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Discrete molecular dynamics studies of the folding of a protein-like model.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Sub-angstrom modeling of complexes between flexible peptides and globular proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

RosettaLigand docking with full ligand and receptor flexibility.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Multiple and single binding modes of fragment-like kinase inhibitors revealed by molecular modeling, residue type-selective protonation, and nuclear overhauser effects

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Role of electrostatic interactions in PDZ domain ligand recognition

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Contributions to the binding free energy of ligands to avidin and streptavidin.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Fast prediction and visualization of protein binding pockets with PASS.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3240807

Role of electrostatic interactions in transient encounter complexes in protein-protein association investigated by paramagnetic relaxation enhancement

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22153506

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22153506

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.STR.2011.09.014

1 reference

15 September 2017

1 reference

15 September 2017

1 reference

PMCID

3240807