(Q34744726)

4 August 2017

title

Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein (English)

1 reference

4 August 2017

1 reference

Karl N Kirschner

1

1 reference

4 August 2017

Katrina W Lexa

2

1 reference

4 August 2017

Amanda M Salisburg

3

1 reference

4 August 2017

Katherine A Alser

4

1 reference

4 August 2017

Leroy Joseph

5

1 reference

4 August 2017

Thomas T Andersen

6

1 reference

4 August 2017

James A Bennett

7

1 reference

4 August 2017

Herbert I Jacobson

8

1 reference

4 August 2017

George C Shields

9

1 reference

4 August 2017

language of work or name

English

0 references

publication date

19 April 2007

1 reference

Journal of the American Chemical Society

4 August 2017

published in

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4 August 2017

volume

129

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4 August 2017

issue

19

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4 August 2017

page(s)

6263-6268

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Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field

4 August 2017

cites work

1 reference

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Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

7 July 2018

1 reference

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Secondary structure provides a template for the folding of nearby polypeptides

7 July 2018

1 reference

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Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations

7 July 2018

1 reference

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Force field influences in beta-hairpin folding simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Ligand-release pathways in the pheromone-binding protein of Bombyx mori

7 July 2018

1 reference

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Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Comparison of multiple Amber force fields and development of improved protein backbone parameters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Model systems for beta-hairpins and beta-sheets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Effects of solvent on the structure of the Alzheimer amyloid-beta(25-35) peptide

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Folding, misfolding, and amyloid protofibril formation of WW domain FBP28.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Amyloid beta-protein monomer structure: a computational and experimental study.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Folding mechanism of beta-hairpins studied by replica exchange molecular simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Prevention of N-methyl-N-nitrosourea-induced breast cancer by alpha-fetoprotein (AFP)-derived peptide, a peptide derived from the active site of AFP

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

The Amber biomolecular simulation programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Free energy landscapes for amyloidogenic tetrapeptides dimerization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Folding cooperativity in a three-stranded beta-sheet model

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Theoretical model of prion propagation: a misfolded protein induces misfolding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

How well can simulation predict protein folding kinetics and thermodynamics?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Simulations of the pressure and temperature unfolding of an alpha-helical peptide.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Protein folding pathways from replica exchange simulations and a kinetic network model

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Synthetic peptide derived from alpha-fetoprotein inhibits growth of human breast cancer: investigation of the pharmacophore and synthesis optimization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Trp-cage: Folding free energy landscape in explicit water

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

A peptide derived from alpha-fetoprotein prevents the growth of estrogen-dependent human breast cancers sensitive and resistant to tamoxifen

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

The free energy landscape for beta hairpin folding in explicit water

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Generalized-ensemble algorithms for molecular simulations of biopolymers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Alpha-fetoprotein structure and function: relevance to isoforms, epitopes, and conformational variants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Studies on a growth-inhibitory peptide derived from alpha-fetoprotein and some analogs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Prediction of tight turns and their types in proteins.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Alpha-fetoprotein-derived antiestrotrophic octapeptide

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Alpha-fetoprotein derived from a human hepatoma prevents growth of estrogen-dependent human breast cancer xenografts

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Levels of maternal serum alpha-fetoprotein (AFP) in pregnant women and subsequent breast cancer risk

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Growth-regulative activity of human alpha-fetoprotein for different types of tumor and normal cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Alpha-fetoprotein in ontogenesis and its association with malignant tumors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Folding landscapes of the Alzheimer amyloid-beta(12-28) peptide.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Mechanical unfolding of segment-swapped protein G dimer: results from replica exchange molecular dynamics simulations.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Protein folding kinetics and thermodynamics from atomistic simulations.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Structure of the 21-30 fragment of amyloid beta-protein.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Optimized parallel tempering simulations of proteins.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Aggregation of polyalanine in a hydrophobic environment.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Conformationally sampled pharmacophore for peptidic delta opioid ligands.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Convergence of replica exchange molecular dynamics.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Structures of a peptide fragment of beta2-microglobulin studied by replica-exchange molecular dynamics simulations - towards the understanding of the mechanism of amyloid formation.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Structure and energy landscape of a photoswitchable peptide: a replica exchange molecular dynamics study

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Atomic simulations of protein folding, using the replica exchange algorithm.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Development of a synthetic cyclized peptide derived from alpha-fetoprotein that prevents the growth of human breast cancer

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Studies on analogs of a peptide derived from alpha-fetoprotein having antigrowth properties

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272344

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

9 December 2018

1 reference

12 December 2020

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

1 reference

12 December 2020

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

1 reference

12 December 2020

Alpha-fetoprotein receptors in a human breast cancer cell line

1 reference

12 December 2020

Amyloid beta-peptide oligomerization in silico: dimer and trimer

1 reference

12 December 2020

Free energy surfaces of miniproteins with a betabetaalpha motif: replica exchange molecular dynamics simulation with an implicit solvation model

1 reference

12 December 2020

Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer

1 reference

12 December 2020

Denatured proteins and early folding intermediates simulated in a reduced conformational space

1 reference

12 December 2020

Ultrafast folding of a computationally designed Trp-cage mutant: Trp2-cage

1 reference

12 December 2020

Energetics and stability of transmembrane helix packing: a replica-exchange simulation with a knowledge-based membrane potential

1 reference

12 December 2020

Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model

1 reference

12 December 2020

Inhibition of estrogen-dependent breast cancer growth by a reaction product of alpha-fetoprotein and estradiol

1 reference

12 December 2020

The recombinant third domain of human alpha-fetoprotein retains the antiestrotrophic activity found in the full-length molecule

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA070202W

1 reference

4 August 2017

1 reference

4 August 2017

1 reference