Toward amino acid typing for proteins in FFLUX

Multipolar Electrostatic Energy Prediction for all 20 Natural Amino Acids Using Kriging Machine Learning

(2016) Timothy L. Fletcher et al.   Journal of Chemical Theory and Computation

Optimization Algorithms in Optimal Predictions of Atomistic Properties by Kriging

(2016) Nicodemo Di Pasquale et al.   Journal of Chemical Theory and Computation

FEREBUS: Highly parallelized engine for kriging training

(2016) Nicodemo Di Pasquale et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer

(2016) Stuart J Davie et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular simulation by knowledgeable quantum atoms

(2016) Paul L A Popelier   PHYSICA SCRIPTA

QCTFF: On the construction of a novel protein force field

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

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

(2015) Timothy J. Hughes et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of conformationally dependent atomic multipole moments in carbohydrates

(2015) Salvatore Cardamone et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Transferable atoms: an intra-atomic perspective through the study of homogeneous oligopeptides

(2015) Peter Maxwell et al.   MOLECULAR PHYSICS

Transferable kriging machine learning models for the multipolar electrostatics of helical deca-alanine

(2015) Timothy L. Fletcher et al.   THEORETICAL CHEMISTRY ACCOUNTS

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

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

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Multipolar electrostatics

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

Multipolar electrostatics for proteins: Atom-atom electrostatic energies in crambin

(2013) Yongna Yuan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

New Insights in Atom-Atom Interactions for Future Drug Design

(2012) Paul Popelier   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

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

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

Communication: The electrostatic polarization is essential to differentiate the helical propensity in polyalanine mutants

(2011) Caiyi Wei et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate Intermolecular Potentials with Physically Grounded Electrostatics

(2011) Maxim Tafipolsky et al.   Journal of Chemical Theory and Computation

Quantifying the Stabilizing Energy of the Intraprotein Hydrogen Bond Due to Local Mutation

(2011) Chang G. Ji et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intramolecular polarisable multipolar electrostatics from the machine learning method Kriging

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

Effect of amino acid polarization in force field biomolecular calculations

(2010) Alexander V. Mitin   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase

(2010) Yunpeng Lu et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM: The biomolecular simulation program

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

NMR Scalar Coupling Constant Reveals That Intraprotein Hydrogen Bonds Are Dynamically Stabilized by Electronic Polarization

(2009) Chang G. Ji et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electronic Polarization Is Important in Stabilizing the Native Structures of Proteins

(2009) Chang G. Ji et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Developing Polarized Protein-Specific Charges for Protein Dynamics: MD Free Energy Calculation of pKa Shifts for Asp26/Asp20 in Thioredoxin

(2008) Changge Ji et al.   BIOPHYSICAL JOURNAL

Protein Polarization Is Critical to Stabilizing AF-2 and Helix-2′ Domains in Ligand Binding to PPAR-γ

(2008) C. G. Ji et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY