Additive CHARMM36 Force Field for Nonstandard Amino Acids

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

MRP.py: A Parameterizer of Post-Translationally Modified Residues

(2020) Patrick G. Sahrmann et al.   Journal of Chemical Information and Modeling

Parameterization of Unnatural Amino Acids with Azido and Alkynyl R-Groups for Use in Molecular Simulations

(2020) Addison K. Smith et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Advances and Challenges in Cell-Free Incorporation of Unnatural Amino Acids Into Proteins

(2019) Wei Gao et al.   Frontiers in Pharmacology

A Molecular Mechanics Model for Flavins

(2019) Alexey Aleksandrov   JOURNAL OF COMPUTATIONAL CHEMISTRY

A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1

(2018) Arman Mussakhmetov et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics

(2018) A. T. Hagler   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Additive CHARMM force field for naturally occurring modified ribonucleotides

(2016) You Xu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Peroxiredoxin Catalysis at Atomic Resolution

(2016) Arden Perkins et al.   STRUCTURE

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library

(2016) Franziska U. Huschmann et al.   Acta Crystallographica Section F-Structural Biology Communications

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

(2015) K. Vanommeslaeghe et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Robustness in the fitting of molecular mechanics parameters

(2015) Kenno Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank

(2014) John D. Westbrook et al.   BIOINFORMATICS

Small molecule annotation for the Protein Data Bank

(2014) S. Sen et al.   Database-The Journal of Biological Databases and Curation

Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis

(2014) Seok Hoon Hong et al.   Frontiers in Chemistry

The path of lysine to pyrrolysine

(2013) Joseph A Krzycki   CURRENT OPINION IN CHEMICAL BIOLOGY

Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data

(2013) Lei Huang et al.   Journal of Chemical Theory and Computation

Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications

(2013) George A. Khoury et al.   Journal of Chemical Theory and Computation

Chemical approaches to detect and analyze protein sulfenic acids

(2013) Cristina M. Furdui et al.   MASS SPECTROMETRY REVIEWS

Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

(2013) Christian Margreitter et al.   NUCLEIC ACIDS RESEARCH

A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications

(2013) Drazen Petrov et al.   PLoS Computational Biology

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

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

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

Expanding molecular modeling and design tools to non-natural sidechains

(2012) David Gfeller et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

SwissSidechain: a molecular and structural database of non-natural sidechains

(2012) David Gfeller et al.   NUCLEIC ACIDS RESEARCH

Structural and Kinetic Isotope Effect Studies of Nicotinamidase (Pnc1) from Saccharomyces cerevisiae

(2011) Brian C. Smith et al.   BIOCHEMISTRY

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

SwissParam: A fast force field generation tool for small organic molecules

(2011) Vincent Zoete et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

(2011) Stuart A. Sievers et al.   NATURE

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

(2011) George A. Khoury et al.   Scientific Reports

Adding New Chemistries to the Genetic Code

(2010) Chang C. Liu et al.   Annual Review of Biochemistry

Characterization of Nicotinamidases: Steady State Kinetic Parameters, Classwide Inhibition by Nicotinaldehydes, and Catalytic Mechanism

(2010) Jarrod B. French et al.   BIOCHEMISTRY

High-Resolution Crystal Structures ofStreptococcus pneumoniaeNicotinamidase with Trapped Intermediates Provide Insights into the Catalytic Mechanism and Inhibition by Aldehydes,

(2010) Jarrod B. French et al.   BIOCHEMISTRY

Force field parameters for the simulation of modified histone tails

(2010) Cédric Grauffel et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

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

Discovering mechanisms of signaling-mediated cysteine oxidation

(2008) Leslie B Poole et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Tet Repressor Induction by Tetracycline: A Molecular Dynamics, Continuum Electrostatics, and Crystallographic Study

(2008) Alexey Aleksandrov et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Dynamics Simulations of the 30S Ribosomal Subunit Reveal a Preferred Tetracycline Binding Site

(2008) Alexey Aleksandrov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY