4.3 Article

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biophysics

Residue-Specific α-Helix Propensities from Molecular Simulation

Robert B. Best et al.

BIOPHYSICAL JOURNAL (2012)

Article Biochemistry & Molecular Biology

Atomistic molecular simulations of protein folding

Robert B. Best

CURRENT OPINION IN STRUCTURAL BIOLOGY (2012)

Article Chemistry, Physical

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

Kyle A. Beauchamp et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Chemistry, Organic

Diastereomer Configurations from Joint Experimental-Computational Analysis

Abil E. Aliev et al.

JOURNAL OF ORGANIC CHEMISTRY (2012)

Article Chemistry, Physical

Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins

Da-Wei Li et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Biochemistry & Molecular Biology

The structure of human ubiquitin in 2-methyl-2,4-pentanediol: A new conformational switch

Kuo Ying Huang et al.

PROTEIN SCIENCE (2011)

Review Chemistry, Organic

Quantum Mechanical Calculation of NMR Parameters in the Stereostructural Determination of Natural Products

Simone Di Micco et al.

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY (2010)

Article Chemistry, Physical

Experimental Verification of Force Fields for Molecular Dynamics Simulations Using Gly-Pro-Gly-Gly

Abil E. Aliev et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Chemistry, Physical

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Jeffery B. Klauda et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Biophysics

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

Lauren Wickstrom et al.

BIOPHYSICAL JOURNAL (2009)

Article Biochemistry & Molecular Biology

Long-timescale molecular dynamics simulations of protein structure and function

John L. Klepeis et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)

Review Chemistry, Physical

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective

Gustavo de M. Seabra et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2009)

Article Chemistry, Physical

Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides

Robert B. Best et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Article Biophysics

Are current molecular dynamics force fields too helical?

Robert B. Best et al.

BIOPHYSICAL JOURNAL (2008)

Article Chemistry, Physical

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Berk Hess et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Chemistry, Physical

On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: Aqueous glycerol

Austin B. Yongye et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2008)

Article Biochemistry & Molecular Biology

NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops

Jan Ferner et al.

NUCLEIC ACIDS RESEARCH (2008)

Review Chemistry, Physical

The quantum-chemical calculation of NMR indirect spin-spin coupling constants

Trygve Helgaker et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2008)

Article Chemistry, Physical

Conformational analysis of L-prolines in water

Abil E. Aliev et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Article Chemistry, Physical

Force field modeling of amino acid conformational energies

Jakub Kaminsky et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Article Chemistry, Physical

Computational NMR spectroscopy: reversing the information flow

Alessandro Bagno et al.

THEORETICAL CHEMISTRY ACCOUNTS (2007)

Article Multidisciplinary Sciences

A consensus view of protein dynamics

Manuel Rueda et al.

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

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Biochemistry & Molecular Biology

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

Viktor Hornak et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Chemistry, Multidisciplinary

Highly stable cyclic dimers based on non-covalent interactions

Valerie G. H. Lafitte et al.

CHEMICAL COMMUNICATIONS (2006)

Article Biochemistry & Molecular Biology

Solid-state NMR studies of collagen-based parchments and gelatin

AE Aliev

BIOPOLYMERS (2005)

Review Chemistry, Multidisciplinary

Empirical force fields for biological macromolecules: Overview and issues

AD Mackerell

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Chemistry, Multidisciplinary

Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model

M Cossi et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)

Article Chemistry, Multidisciplinary

Binding site optimisation for artificial enzymes by diffusion NMR of small molecules

CE Atkinson et al.

CHEMISTRY-A EUROPEAN JOURNAL (2003)

Review Biochemistry & Molecular Biology

Molecular dynamics simulations of biomolecules

M Karplus et al.

NATURE STRUCTURAL BIOLOGY (2002)

Article Chemistry, Multidisciplinary

Modern protein force fields behave comparably in molecular dynamics simulations

DJ Price et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)

Article Biochemistry & Molecular Biology

Conformational preferences of substituted prolines in the collagen triple helix

SD Mooney et al.

BIOPOLYMERS (2002)

Article Multidisciplinary Sciences

α-Helical stabilization by side chain shielding of backbone hydrogen bonds

AE García et al.

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

Article Chemistry, Multidisciplinary

Static and dynamic effects on vicinal scalar J couplings in proteins and peptides:: A MD/DFT analysis

DA Case et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2000)