Related references
Note: Only part of the references are listed.Ranking Reversible Covalent Drugs: From Free Energy Perturbation to Fragment Docking
Han Zhang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology
Matthias Gehringer et al.
JOURNAL OF MEDICINAL CHEMISTRY (2019)
Software update: the ORCA program system, version 4.0
Frank Neese
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2018)
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator
Fang-Yu Lin et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
Communication: Correct charge transfer in CT complexes from the Becke'05 density functional
Axel D. Becke et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
NAMD goes quantum: an integrative suite for hybrid simulations
Marcelo C. R. Melo et al.
NATURE METHODS (2018)
L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib
D. Callegari et al.
CHEMICAL SCIENCE (2018)
Pervasive Delocalisation Error Causes Spurious Proton Transfer in Organic Acid-Base Co-Crystals
Luc M. LeBlanc et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)
How Reactive are Druggable Cysteines in Protein Kinases?
Ernest Awoonor-Williams et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
The hydration structure of methylthiolate from QM/MM molecular dynamics
Ernest Awoonor-Williams et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
Mechanisms of Alkyl and Aryl Thiol Addition to N-Methylmaleimide
Mark A. R. Raycroft et al.
JOURNAL OF ORGANIC CHEMISTRY (2018)
Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions
Paul A. Jackson et al.
JOURNAL OF MEDICINAL CHEMISTRY (2017)
Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity
Richard Lonsdale et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Interrogating the Becke'05 density functional for non-locality information
Stephen G. Dale et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction
Sarah R. Whittleton et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?
Payal Chatterjee et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)
Quantification and Theoretical Analysis of the Electrophilicities of Michael Acceptors
Dominik S. Allgaeuer et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)
Modeling covalent-modifier drugs
Ernest Awoonor-Williams et al.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2017)
Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins
Ernest Awoonor-Williams et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Quantum Mechanics/Molecular Mechanics Modeling of Covalent Addition between EGFR-Cysteine 797 and N-(4-Anilinoquinazolin-6-yl) Acrylamide
Luigi Capoferri et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
Automated computational screening of the thiol reactivity of substituted alkenes
Jennifer M. Smith et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2015)
Systematic Study of the Glutathione (GSH) Reactivity of N-Arylacrylamides: 1. Effects of Aryl Substitution
Victor J. Cee et al.
JOURNAL OF MEDICINAL CHEMISTRY (2015)
Improved DFT Potential Energy Surfaces via Improved Densities
Min-Cheol Kim et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2015)
Prolonged and tunable residence time using reversible covalent kinase inhibitors
J. Michael Bradshaw et al.
NATURE CHEMICAL BIOLOGY (2015)
Ions in solution: Density corrected density functional theory (DC-DFT)
Min-Cheol Kim et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Perspective: Fifty years of density-functional theory in chemical physics
Axel D. Becke
JOURNAL OF CHEMICAL PHYSICS (2014)
Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications
Michael Gaus et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
The CHARMM-TURBOMOLE Interface for Efficient and Accurate QM/MM Molecular Dynamics, Free Energies, and Excited State Properties
Saleh Riahi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
Chemical and Computational Methods for the Characterization of Covalent Reactive Groups for the Prospective Design of Irreversible Inhibitors
Mark E. Flanagan et al.
JOURNAL OF MEDICINAL CHEMISTRY (2014)
Benchmarking Quantum Chemical Methods for the Calculation of Molecular Dipole Moments and Polarizabilities
A. Leif Hickey et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2014)
Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field
Yun Luo et al.
FARADAY DISCUSSIONS (2013)
Computational study of the covalent bonding of microcystins to cysteine residues - a reaction involved in the inhibition of the PPP family of protein phosphatases
Susana R. Pereira et al.
FEBS JOURNAL (2013)
Non-covalent interactions and thermochemistry using XDM-corrected hybrid and range-separated hybrid density functionals
A. Otero-de-la-Roza et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Extreme density-driven delocalization error for a model solvated-electron system
Erin R. Johnson et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Communication: Electronic structure of the solvated chloride anion from first principles molecular dynamics
Cui Zhang et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Range-Separated DFT Functionals are Necessary to Model Thio-Michael Additions
Jennifer M. Smith et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data
Lei Huang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters
James J. P. Stewart
JOURNAL OF MOLECULAR MODELING (2013)
Understanding and Reducing Errors in Density Functional Calculations
Min-Cheol Kim et al.
PHYSICAL REVIEW LETTERS (2013)
Mechanistic insights into N- or P-centered nucleophile promoted thiol-vinylsulfone Michael addition
Chen Wang et al.
TETRAHEDRON (2013)
Modified Becke'05 method of nondynamic correlation in density functional theory with self-consistent implementation
Emil Proynov et al.
CHEMICAL PHYSICS LETTERS (2012)
Improved self-consistent and resolution-of-identity approximated Becke'05 density functional model of nondynamic electron correlation
Emil Proynov et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
The Solvation Structure of Na+ and K+ in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations
Christopher N. Rowley et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Why are the Interaction Energies of Charge-Transfer Complexes Challenging for DFT?
Stephan N. Steinmann et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Reversible targeting of noncatalytic cysteines with chemically tuned electrophiles
Iana M. Serafimova et al.
NATURE CHEMICAL BIOLOGY (2012)
The ORCA program system
Frank Neese
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2012)
DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
Michael Gaus et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Evaluating the Performance of DFT Functionals in Assessing the Interaction Energy and Ground-State Charge Transfer of Donor/Acceptor Complexes: Tetrathiafulvalene-Tetracyanoquinodimethane (TTF-TCNQ) as a Model Case
Gjergji Sini et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Effect of the Damping Function in Dispersion Corrected Density Functional Theory
Stefan Grimme et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Transition States and Energetics of Nucleophilic Additions of Thiols to Substituted α,β-Unsaturated Ketones: Substituent Effects Involve Enone Stabilization, Product Branching, and Solvation
Elizabeth H. Krenske et al.
JOURNAL OF ORGANIC CHEMISTRY (2011)
Improving the Accuracy of Hybrid Meta-GGA Density Functionals by Range Separation
Roberto Peverati et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2011)
Predicting Michael-acceptor reactivity and toxicity through quantum chemical transition-state calculations
Denis Mulliner et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2011)
How reliable are DFT transition structures? Comparison of GGA, hybrid-meta-GGA and meta-GGA functionals
Luis Simon et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2011)
van der Waals Interactions in Density-Functional Theory: Intermolecular Complexes
Felix O. Kannemann et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Integration Grid Errors for Meta-GGA-Predicted Reaction Energies: Origin of Grid Errors for the M06 Suite of Functionals
Steven E. Wheeler et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
The Bruton tyrosine kinase inhibitor PCI-32765 blocks B-cell activation and is efficacious in models of autoimmune disease and B-cell malignancy
Lee A. Honigberg et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Efficient, approximate and parallel Hartree-Fock and hybrid DFT calculations. A 'chain-of-spheres' algorithm for the Hartree-Fock exchange
Frank Neese et al.
CHEMICAL PHYSICS (2009)
Anchoring the gas-phase acidity scale: From formic acid to methanethiol
Nicole Eyet et al.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2009)
Oscillations in meta-generalized-gradient approximation potential energy surfaces for dispersion-bound complexes
Erin R. Johnson et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
On the self-consistent implementation of general occupied-orbital dependent exchange-correlation functionals with application to the B05 functional
Alexei V. Arbuznikov et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Van der Waals Interactions in Density-Functional Theory: Rare-Gas Diatomics
Felix O. Kannemann et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Investigation of Exchange Energy Density Functional Accuracy for Interacting Molecules
Eamonn D. Murray et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Covalent Modifiers: An Orthogonal Approach to Drug Design
Michele H. Potashman et al.
JOURNAL OF MEDICINAL CHEMISTRY (2009)
Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions
Christopher J. Fennell et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Hartree-Fock orbitals significantly improve the reaction barrier heights predicted by semilocal density functionals
Benjamin G. Janesko et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections
Jeng-Da Chai et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
6-Ethynylthieno[3,2-d]- and 6-ethynylthieno[2,3-d]pyrimidin-4-anilines as tunable covalent modifiers of ErbB kinases
Edgar R. Wood et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Insights into current limitations of density functional theory
Aron J. Cohen et al.
SCIENCE (2008)
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
Yan Zhao et al.
THEORETICAL CHEMISTRY ACCOUNTS (2008)
Avoiding singularity problems associated with meta-GGA (generalized gradient approximation) exchange and correlation functionals containing the kinetic energy density
Jurgen Grafenstein et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Extension of the self-consistent-charge density-functional tight-binding method: Third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction
Yang Yang et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2007)
DFTB+, a sparse matrix-based implementation of the DFTB method
B. Aradi et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2007)
A comparison of methods to compute the potential of mean force
Daniel Trzesniak et al.
CHEMPHYSCHEM (2007)
Spurious fractional charge on dissociated atoms: Pervasive and resilient self-interaction error of common density functionals
Adrienn Ruzsinszky et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Importance of short-range versus long-range Hartree-Fock exchange for the performance of hybrid density functionals
Oleg A. Vydrov et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Scalable molecular dynamics with NAMD
JC Phillips et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Reaction barrier heights from an exact-exchange-based density-functional correlation model
RM Dickson et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Structural bioinformatics-based design of selective, irreversible kinase inhibitors
MS Cohen et al.
SCIENCE (2005)
A 'universal' B3LYP-based method for gas-phase molecular properties: bond dissociation enthalpy, ionization potential, electron and proton affinity and gas-phase acidity
JS Wright et al.
MOLECULAR PHYSICS (2005)
Real-space post-Hartree-Fock correlation models
AD Becke
JOURNAL OF CHEMICAL PHYSICS (2005)
Synthesis and physicochemical characterization of end-linked poly(ethylene glycol)-co-peptide hydrogels formed by Michael-type addition
MP Lutolf et al.
BIOMACROMOLECULES (2003)
A long-range correction scheme for generalized-gradient-approximation exchange functionals
H Iikura et al.
JOURNAL OF CHEMICAL PHYSICS (2001)
Application of an approximate density-functional method to sulfur containing compounds
TA Niehaus et al.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (2001)
Density functional theory based model calculations for accurate bond dissociation enthalpies. 2. Studies of X-X and X-Y (X, Y=C, N, O, S, halogen) bonds
GA DiLabio et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2000)