Realistic sampling of amino acid geometries for a multipolar polarizable force field

QCTFF: On the construction of a novel protein force field

(2015) Paul L. A. Popelier   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Accurate prediction of polarised high order electrostatic interactions for hydrogen bonded complexes using the machine learning method kriging

(2015) Timothy J. Hughes et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

A fragment based step-by-step strategy for determining the most stable conformers of biomolecules

(2014) Hongbao Li et al.   CHEMICAL PHYSICS LETTERS

Direct computation of parameters for accurate polarizable force fields

(2014) Toon Verstraelen et al.   JOURNAL OF CHEMICAL PHYSICS

Prediction of Intramolecular Polarization of Aromatic Amino Acids Using Kriging Machine Learning

(2014) Timothy L. Fletcher et al.   Journal of Chemical Theory and Computation

Charge Anisotropy: Where Atomic Multipoles Matter Most

(2014) Christian Kramer et al.   Journal of Chemical Theory and Computation

Free Energy Surface Reconstruction from Umbrella Samples Using Gaussian Process Regression

(2014) Thomas Stecher et al.   Journal of Chemical Theory and Computation

Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations

(2014) Michel A. Cuendet et al.   Journal of Chemical Theory and Computation

A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations

(2014) Stefan Grimme   Journal of Chemical Theory and Computation

Efficient parameterization of torsional terms for force fields

(2014) Steven K. Burger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Hydrogen-hydrogen interaction in planar biphenyl: A theoretical study based on the interacting quantum atoms and Hirshfeld atomic energy partitioning methods

(2014) Kiamars Eskandari et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Multipolar electrostatics based on the Kriging machine learning method: an application to serine

(2014) Yongna Yuan et al.   JOURNAL OF MOLECULAR MODELING

Comprehensive Analysis of Energy Minima of the 20 Natural Amino Acids

(2014) Yongna Yuan et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Multipolar electrostatics

(2014) Salvatore Cardamone et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Protein side-chain modeling with a protein-dependent optimized rotamer library

(2014) Patricia Francis-Lyon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL)

(2014) Sabareesh Subramaniam et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The prediction of atomic kinetic energies from coordinates of surrounding atoms using kriging machine learning

(2014) Timothy L. Fletcher et al.   THEORETICAL CHEMISTRY ACCOUNTS

DFT-steric-based energy decomposition analysis of intermolecular interactions

(2014) Dong Fang et al.   THEORETICAL CHEMISTRY ACCOUNTS

Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine

(2013) Shaun M. Kandathil et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Unified approach to multipolar polarisation and charge transfer for ions: microhydrated Na+

(2013) Matthew J. L. Mills et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Machine-learning approach for one- and two-body corrections to density functional theory: Applications to molecular and condensed water

(2013) Albert P. Bartók et al.   PHYSICAL REVIEW B

Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds

(2012) Steven K. Burger et al.   Journal of Chemical Theory and Computation

Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation

(2012) Kresten Lindorff-Larsen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

(2012) Matthias Rupp et al.   PHYSICAL REVIEW LETTERS

Polarisable multipolar electrostatics from the machine learning method Kriging: an application to alanine

(2012) Matthew J. L. Mills et al.   THEORETICAL CHEMISTRY ACCOUNTS

Amino Acids with Hydrogen-Bonding Side Chains have an Intrinsic Tendency to Sample Various Turn Conformations in Aqueous Solution

(2011) Andrew Hagarman et al.   CHEMISTRY-A EUROPEAN JOURNAL

Assessment of the Intrinsic Conformational Preferences of Dipeptide Amino Acids in Aqueous Solution by Combined Umbrella Sampling/MBAR Statistics. A Comparison with Experimental Results

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

Conformational propensities and residual structures in unfolded peptides and proteins

(2011) Reinhard Schweitzer-Stenner   Molecular BioSystems

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Intramolecular polarisable multipolar electrostatics from the machine learning method Kriging

(2011) Matthew J.L. Mills et al.   Computational and Theoretical Chemistry

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Quantifying steric effect with experimental electron density

(2010) Vladimir G. Tsirelson et al.   JOURNAL OF CHEMICAL PHYSICS

Conformations of Phenylalanine in the Tripeptides AFA and GFG Probed by Combining MD Simulations with NMR, FTIR, Polarized Raman, and VCD Spectroscopy

(2010) Silvia Pizzanelli et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of a Rotamer Library for Use in β-Peptide Foldamer Computational Design

(2010) Scott J. Shandler et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water

(2010) Alexander D. Scouras et al.   PROTEIN SCIENCE

Geometrically faithful homeomorphisms between the electron density and the bare nuclear potential

(2009) Paul L. A. Popelier et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

“Mindless” DFT Benchmarking

(2009) Martin Korth et al.   Journal of Chemical Theory and Computation

Gas-Phase Geometry Optimization of Biological Molecules as a Reasonable Alternative to a Continuum Environment Description: Fact, Myth, or Fiction?†

(2009) Sérgio Filipe Sousa et al.   JOURNAL OF PHYSICAL CHEMISTRY A

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

Optimal construction of a fast and accurate polarisable water potential based on multipole moments trained by machine learning

(2009) Chris M. Handley et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures

(2009) Yunqi Li et al.   PLoS One

The importance of multipole moments when describing water and hydrated amino acid cluster geometry

(2008) Majeed Shaik et al.   MOLECULAR PHYSICS

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