4.7 Article

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

Related references

Note: Only part of the references are listed.
Article Chemistry, Physical

Conformational free energies of methyl-α-L-iduronic and methyl-β-D-glucuronic acids in water

Volodymyr Babin et al.

JOURNAL OF CHEMICAL PHYSICS (2010)

Article Chemistry, Physical

Adaptively Biased Molecular Dynamics: An Umbrella Sampling Method With a Time-Dependent Potential

Volodymyr Babin et al.

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (2009)

Article Chemistry, Physical

Theoretical Studies of Short Polyproline Systems: Recalibration of a Molecular Ruler

Elena Dolghih et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2009)

Article Multidisciplinary Sciences

Conformations and free energy landscapes of polyproline peptides

Mahmoud Moradi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biophysics

Are current molecular dynamics force fields too helical?

Robert B. Best et al.

BIOPHYSICAL JOURNAL (2008)

Article Chemistry, Physical

Adaptively biased molecular dynamics for free energy calculations

Volodymyr Babin et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Multidisciplinary Sciences

Effect of flexibility and cis residues in single-molecule FRET studies of polyproline

Robert B. Best et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Probing polyproline structure and dynamics by photoinduced electron transfer provides evidence for deviations from a regular polyproline type II helix

Soeren Doose et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Chemistry, Physical

Puckering transition of proline residue in water

Young Kee Kang

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Article Chemistry, Multidisciplinary

A 10-Å spectroscopic ruler applied to short polyprolines

Harekrushna Sahoo et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Multidisciplinary Sciences

The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations

Reinhard Schweitzer-Stenner et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Chemistry, Physical

Computation of free energy profiles with parallel adaptive dynamics

Tony Lelievre et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Biophysics

Further evidence for the absence of polyproline II stretch in the XAO peptide

Joanna Makowska et al.

BIOPHYSICAL JOURNAL (2007)

Article Chemistry, Multidisciplinary

Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study

Juergen Graf et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Chemistry, Physical

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

Volodymyr Babin et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Physical

Conformational preferences of proline oligopeptides

Young Kee Kang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Chemistry, Physical

Quantitative single-molecule conformational distributions: A case study with poly-(L-proline)

LP Watkins et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2006)

Article Physics, Multidisciplinary

Equilibrium free energies from nonequilibrium metadynamics

G Bussi et al.

PHYSICAL REVIEW LETTERS (2006)

Article Chemistry, Physical

Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics

P Raiteri et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Chemistry, Multidisciplinary

Demonstration of the ring conformation in polyproline by the Raman optical activity

J Kapitán et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Chemistry, Physical

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations

JG Lee et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Multidisciplinary Sciences

Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins

J Makowska et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales

ZS Shi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Chemistry, Physical

Exploring intramolecular reactions in complex systems with metadynamics: The case of the malonate anions

E Asciutto et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2005)

Article Multidisciplinary Sciences

Unusual compactness of a polyproline type II structure

B Zagrovic et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Chemistry, Physical

Hydration structure of Y3+ and La3+ compared:: An application of metadynamics -: art. no. 244507

T Ikeda et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Chemistry, Multidisciplinary

Flexible docking in solution using metadynamics

FL Gervasio et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Multidisciplinary Sciences

Polyproline and the spectroscopic ruler revisited with single-molecule fluorescence

B Schuler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Polymer Science

On the stability of polyproline-I and II structures of proline oligopeptides

S Kakinoki et al.

POLYMER BULLETIN (2005)

Article Chemistry, Multidisciplinary

Vibrational Raman optical activity characterization of poly(L-proline) II helix in alanine oligopeptides

IH McColl et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Biochemistry & Molecular Biology

Cis-trans isomerization and puckering of proline residue

YK Kang et al.

BIOPHYSICAL CHEMISTRY (2004)

Article Chemistry, Multidisciplinary

A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion

B Ensing et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Chemistry, Physical

Ab initio study of dehydroxylation-carbonation reaction on brucite surface

SV Churakov et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2004)

Article Physics, Multidisciplinary

Proton transfer in heterocycle crystals

M Iannuzzi et al.

PHYSICAL REVIEW LETTERS (2004)

Article Multidisciplinary Sciences

Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution

F Eker et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biophysics

Microscopic mechanism of antibiotics translocation through a porin

M Ceccarelli et al.

BIOPHYSICAL JOURNAL (2004)

Article Biochemistry & Molecular Biology

Short sequences of non-proline residues can adopt the polyproline II helical conformation

BW Chellgren et al.

BIOCHEMISTRY (2004)

Article Biochemistry & Molecular Biology

Polyproline II helix is the preferred conformation for unfolded polyalanine in water

M Mezei et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)

Article Physics, Multidisciplinary

Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods

MR Shirts et al.

PHYSICAL REVIEW LETTERS (2003)

Article Biochemistry & Molecular Biology

Host-guest scale of left-handed polyproline II helix formation

AL Rucker et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)

Article Chemistry, Multidisciplinary

Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy

F Eker et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Physics, Multidisciplinary

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics

M Iannuzzi et al.

PHYSICAL REVIEW LETTERS (2003)

Article Biochemistry & Molecular Biology

A simple model for polyproline II structure in unfolded states of alanine-based peptides

RV Pappu et al.

PROTEIN SCIENCE (2002)

Article Biochemistry & Molecular Biology

Proline cis-trans isomerization and protein folding

WJ Wedemeyer et al.

BIOCHEMISTRY (2002)

Article Chemistry, Multidisciplinary

Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study

F Eker et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)

Article Multidisciplinary Sciences

Escaping free-energy minima

A Laio et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Multidisciplinary Sciences

Polyproline II structure in a sequence of seven alanine residues

ZS Shi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

Preferred proline puckerings in cis and trans peptide groups:: Implications for collagen stability

L Vitagliano et al.

PROTEIN SCIENCE (2001)

Article Biochemistry & Molecular Biology

Host-guest study of left-handed polyproline II helix formation

MA Kelly et al.

BIOCHEMISTRY (2001)

Article Chemistry, Physical

Calculating free energies using average force

E Darve et al.

JOURNAL OF CHEMICAL PHYSICS (2001)

Article Physics, Multidisciplinary

Efficient, multiple-range random walk algorithm to calculate the density of states

FG Wang et al.

PHYSICAL REVIEW LETTERS (2001)

Article Chemistry, Physical

Multidimensional replica-exchange method for free-energy calculations

Y Sugita et al.

JOURNAL OF CHEMICAL PHYSICS (2000)

Article Physics, Fluids & Plasmas

Path-ensemble averages in systems driven far from equilibrium

GE Crooks

PHYSICAL REVIEW E (2000)