Intrinsic α-helical and β-sheet conformational preferences: A computational case study of alanine

New Insights into the Interdependence between Amino Acid Stereochemistry and Protein Structure

(2013) Alice Qinhua Zhou et al.   BIOPHYSICAL JOURNAL

pH-Independence of Trialanine and the Effects of Termini Blocking in Short Peptides: A Combined Vibrational, NMR, UVCD, and Molecular Dynamics Study

(2013) Siobhan Toal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Power of Hard-Sphere Models: Explaining Side-Chain Dihedral Angle Distributions of Thr and Val

(2012) Alice Qinhua Zhou et al.   BIOPHYSICAL JOURNAL

Critical Assessment of Current Force Fields. Short Peptide Test Case

(2012) Jiří Vymětal et al.   Journal of Chemical Theory and Computation

The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development

(2012) Fan Jiang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology

(2011) Francisco F. García-Prieto et al.   JOURNAL OF CHEMICAL PHYSICS

Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

(2011) Paul S. Nerenberg et al.   Journal of Chemical Theory and Computation

UsingJ-Coupling Constants for Force Field Validation: Application to Hepta-alanine

(2011) Panagiota S. Georgoulia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water-Mediated Conformations of the Alanine Dipeptide as Revealed by Distributed Umbrella Sampling Simulations, Quantum Mechanics Based Calculations, and Experimental Data

(2011) Víctor Cruz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Revisiting the Ramachandran plot from a new angle

(2011) Alice Qinhua Zhou et al.   PROTEIN SCIENCE

NMR-Based Protein Potentials

(2010) Da-Wei Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water: Singular value decomposition analysis

(2010) Kwang-Im Oh et al.   CHIRALITY

Taming the complexity of protein folding

(2010) Gregory R Bowman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

(2010) Pär Bjelkmar et al.   Journal of Chemical Theory and Computation

UV Resonance Raman Investigation of the Conformations and Lowest Energy Allowed Electronic Excited States of Tri- and Tetraalanine: Charge Transfer Transitions

(2010) Bhavya Sharma et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach

(2010) Ryosuke Ishizuka et al.   Journal of Physical Chemistry Letters

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Distribution of Conformations Sampled by the Central Amino Acid Residue in Tripeptides Inferred From Amide I Band Profiles and NMR Scalar Coupling Constants

(2009) Reinhard Schweitzer-Stenner   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intrinsic Propensities of Amino Acid Residues in GxG Peptides Inferred from Amide I′ Band Profiles and NMR Scalar Coupling Constants

(2009) Andrew Hagarman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational Properties of a Peptide Model for Unfolded α-Helices†

(2008) Angela M. Firestine et al.   BIOCHEMISTRY

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with IR and vibrational circular dichroism spectra

(2008) Kijeong Kwac et al.   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Determination of Conformational Preferences of Dipeptides Using Vibrational Spectroscopy

(2008) Jože Grdadolnik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins

(2008) D. A. C. Beck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA