Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field

Development and Testing of Force Field Parameters for Phenylalanine and Tyrosine Derivatives

(2021) Xiaowen Wang et al.   Frontiers in Molecular Biosciences

Machine Learning Force Fields

(2021) Oliver T. Unke et al.   CHEMICAL REVIEWS

Additive CHARMM36 Force Field for Nonstandard Amino Acids

(2021) Anastasia Croitoru et al.   Journal of Chemical Theory and Computation

19F-NMR reveals substrate specificity of CYP121A1 in Mycobacterium tuberculosis

(2021) Christopher S. Campomizzi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids

(2021) John P. Stoppelman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Small, but powerful and attractive: 19F in biomolecular NMR

(2021) Angela M. Gronenborn   STRUCTURE

Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers

(2020) Falk Hoffmann et al.   JOURNAL OF CHEMICAL PHYSICS

What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein

(2020) Hannah Welte et al.   Scientific Reports

Rapid Quantification of Protein-Ligand Binding via 19F NMR Lineshape Analysis

(2020) Samantha S. Stadmiller et al.   BIOPHYSICAL JOURNAL

Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field

(2020) Fang-Yu Lin et al.   Journal of Chemical Theory and Computation

A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics

(2020) Anthony T. Bogetti et al.   JOURNAL OF CHEMICAL PHYSICS

The ORCA quantum chemistry program package

(2020) Frank Neese et al.   JOURNAL OF CHEMICAL PHYSICS

Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens

(2020) Christian Devereux et al.   Journal of Chemical Theory and Computation

A fast and high-quality charge model for the next generation general AMBER force field

(2020) Xibing He et al.   JOURNAL OF CHEMICAL PHYSICS

OrbNet: Deep learning for quantum chemistry using symmetry-adapted atomic-orbital features

(2020) Zhuoran Qiao et al.   JOURNAL OF CHEMICAL PHYSICS

Solution NMR readily reveals distinct structural folds and interactions in doubly 13C- and 19F-labeled RNAs

(2020) Owen B. Becette et al.   Science Advances

Aromatic 19F-13C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics

(2019) Andras Boeszoermenyi et al.   NATURE METHODS

19F Dynamic Nuclear Polarization at Fast Magic Angle Spinning for NMR of HIV-1 Capsid Protein Assemblies

(2019) Manman Lu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Side-Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations

(2019) Suad Rashid et al.   JOURNAL OF PHYSICAL CHEMISTRY B

19F NMR relaxation studies of fluorosubstituted tryptophans

(2019) Manman Lu et al.   JOURNAL OF BIOMOLECULAR NMR

Effect of Noncanonical Amino Acids on Protein–Carbohydrate Interactions: Structure, Dynamics, and Carbohydrate Affinity of a Lectin Engineered with Fluorinated Tryptophan Analogs

(2018) Felix Tobola et al.   ACS Chemical Biology

Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields

(2018) Falk Hoffmann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors

(2018) Manman Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Narrowing the gap between experimental and computational determination of methyl group dynamics in proteins

(2018) Falk Hoffmann et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ligand-Based Fluorine NMR Screening: Principles and Applications in Drug Discovery Projects

(2018) Claudio Dalvit et al.   JOURNAL OF MEDICINAL CHEMISTRY

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

(2017) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evaluating amber force fields using computed NMR chemical shifts

(2017) David R. Koes et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost

(2017) J. S. Smith et al.   Chemical Science

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

The Multiple Origins of the Hydrophobicity of Fluorinated Apolar Amino Acids

(2017) João Ramiro Robalo et al.   Chem

Fluorine nuclear magnetic resonance-based assay in living mammalian cells

(2016) Marina Veronesi et al.   ANALYTICAL BIOCHEMISTRY

Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study

(2016) Naima G. Sharaf et al.   BIOCHEMISTRY

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

(2016) Karl T. Debiec et al.   Journal of Chemical Theory and Computation

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

(2016) Michael R. Shirts et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein-Observed Fluorine NMR: A Bioorthogonal Approach for Small Molecule Discovery

(2015) Keith E. Arntson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Using 19F NMR to Probe Biological Interactions of Proteins and Peptides

(2014) E. Neil G. Marsh et al.   ACS Chemical Biology

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

(2014) David S. Cerutti et al.   Journal of Chemical Theory and Computation

Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

(2014) Karl T. Debiec et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fluorine-19 NMR of integral membrane proteins illustrated with studies of GPCRs

(2013) Tatiana Didenko et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization

(2013) David S. Cerutti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simple and inexpensive incorporation of 19F-Tryptophan for protein NMR spectroscopy

(2012) Peter B. Crowley et al.   CHEMICAL COMMUNICATIONS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Water Model Tuning for Improved Reproduction of Rotational Diffusion and NMR Spectral Density

(2012) Kazuhiro Takemura et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

(2012) Marcus D Hanwell et al.   Journal of Cheminformatics

GPU-accelerated molecular modeling coming of age

(2010) John E. Stone et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein19F NMR inEscherichia coli

(2009) Conggang Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hidden alternative structures of proline isomerase essential for catalysis

(2009) James S. Fraser et al.   NATURE

Effects of tryptophan residue fluorination on streptavidin stability and biotin–streptavidin interactions via molecular dynamics simulations

(2008) Jarosław J. Panek et al.   JOURNAL OF MOLECULAR MODELING

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide-plane flipping in proteins

(2002) Steven Hayward   PROTEIN SCIENCE