The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations
出版年份 2019 全文链接
标题
The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations
作者
关键词
-
出版物
MOLECULES
Volume 24, Issue 4, Pages 681
出版商
MDPI AG
发表日期
2019-02-15
DOI
10.3390/molecules24040681
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Survival of the most transferable at the top of Jacob’s ladder: Defining and testing the ωB97M(2) double hybrid density functional
- (2018) Narbe Mardirossian et al. JOURNAL OF CHEMICAL PHYSICS
- Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model
- (2018) Matthew P. Kroonblawd et al. Journal of Chemical Theory and Computation
- Revised M06 density functional for main-group and transition-metal chemistry
- (2018) Ying Wang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages
- (2018) Hannes H. Loeffler et al. Journal of Chemical Theory and Computation
- Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching
- (2018) Phillip S. Hudson et al. Journal of Chemical Theory and Computation
- Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation
- (2018) Pengfei Li et al. Journal of Chemical Theory and Computation
- Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies
- (2017) Martin A. Olsson et al. Journal of Chemical Theory and Computation
- How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging
- (2017) Ulf Ryde Journal of Chemical Theory and Computation
- Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities
- (2017) Fiona L. Kearns et al. JOURNAL OF COMPUTATIONAL 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
- Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals
- (2017) Narbe Mardirossian et al. MOLECULAR PHYSICS
- Revised M06-L functional for improved accuracy on chemical reaction barrier heights, noncovalent interactions, and solid-state physics
- (2017) Ying Wang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Synthesis and bioactivities of novel pyrazole oxime derivatives containing a 1,2,3-thiadiazole moiety
- (2016) Hong Dai et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Novel 1,3,4-oxadiazole/oxime hybrids: Synthesis, docking studies and investigation of anti-inflammatory, ulcerogenic liability and analgesic activities
- (2016) Heba S. Abd-Ellah et al. BIOORGANIC CHEMISTRY
- Discovery of Chromeno[4,3-c]pyrazol-4(2H)-one Containing Carbonyl or Oxime Derivatives as Potential, Selective Inhibitors PI3Kα
- (2016) Liang Lu et al. CHEMICAL & PHARMACEUTICAL BULLETIN
- Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods
- (2016) Ulf Ryde et al. CHEMICAL REVIEWS
- Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation
- (2016) Yuezhi Mao et al. JOURNAL OF CHEMICAL PHYSICS
- Blind test of density-functional-based methods on intermolecular interaction energies
- (2016) DeCarlos E. Taylor et al. JOURNAL OF CHEMICAL PHYSICS
- ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation
- (2016) Narbe Mardirossian et al. JOURNAL OF CHEMICAL PHYSICS
- Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge
- (2016) Caitlin C. Bannan et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Convergence of single-step free energy perturbation
- (2016) Stefan Boresch et al. MOLECULAR PHYSICS
- QM/MM free energy simulations: recent progress and challenges
- (2016) Xiya Lu et al. MOLECULAR SIMULATION
- MN15: A Kohn–Sham global-hybrid exchange–correlation density functional with broad accuracy for multi-reference and single-reference systems and noncovalent interactions
- (2016) Haoyu S. Yu et al. Chemical Science
- Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations
- (2015) Gerhard König et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes
- (2015) Phillip S. Hudson et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Indirubin 3′-( O -oxiran-2-ylmethyl)oxime: A novel anticancer agent
- (2015) Yoshimi Ichimaru et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching
- (2015) Jicun Li et al. JOURNAL OF CHEMICAL PHYSICS
- Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm
- (2015) Samuel Manzer et al. JOURNAL OF CHEMICAL PHYSICS
- Mapping the genome of meta-generalized gradient approximation density functionals: The search for B97M-V
- (2015) Narbe Mardirossian et al. JOURNAL OF CHEMICAL PHYSICS
- A “Stepping Stone” Approach for Obtaining Quantum Free Energies of Hydration
- (2015) Chris Sampson et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems
- (2015) Phillip S. Hudson et al. Journal of Physical Chemistry Letters
- Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design
- (2014) Yuri Pevzner et al. Journal of Chemical Information and Modeling
- Achieving High-Accuracy Intermolecular Interactions by Combining Coulomb-Attenuated Second-Order Møller–Plesset Perturbation Theory with Coupled Kohn–Sham Dispersion
- (2014) Yuanhang Huang et al. Journal of Chemical Theory and Computation
- Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
- (2014) Gerhard König et al. Journal of Chemical Theory and Computation
- Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations
- (2014) Yan Zhou et al. Journal of Chemical Theory and Computation
- Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge
- (2014) Samuel Genheden et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Separate Electronic Attenuation Allowing a Spin-Component-Scaled Second-Order Møller–Plesset Theory to Be Effective for Both Thermochemistry and Noncovalent Interactions
- (2014) Matthew Goldey et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation
- (2014) Christopher Cave-Ayland et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB)
- (2014) Jan Gerit Brandenburg et al. Journal of Physical Chemistry Letters
- Quest for a universal density functional: the accuracy of density functionals across a broad spectrum of databases in chemistry and physics
- (2014) R. Peverati et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
- Density functional tight binding: values of semi-empirical methods in an ab initio era
- (2014) Qiang Cui et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Advances in Binding Free Energies Calculations: QM/MM-Based Free Energy Perturbation Method for Drug Design
- (2013) R.S. Rathore et al. CURRENT PHARMACEUTICAL DESIGN
- Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics
- (2013) Christoph Dellago et al. Entropy
- 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
- ZINC: A Free Tool to Discover Chemistry for Biology
- (2012) John J. Irwin et al. Journal of Chemical Information and Modeling
- A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations
- (2012) Tai-Sung Lee et al. Journal of Chemical Theory and Computation
- Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data
- (2012) Lee-Ping Wang et al. Journal of Chemical Theory and Computation
- The SAMPL3 blind prediction challenge: transfer energy overview
- (2012) Matthew T. Geballe et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Attenuating Away the Errors in Inter- and Intramolecular Interactions from Second-Order Møller–Plesset Calculations in the Small Aug-cc-pVDZ Basis Set
- (2012) Matthew Goldey et al. Journal of Physical Chemistry Letters
- Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
- (2012) Jimmy Heimdal et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Synthesis, crystal structures and luminescent properties of two one-dimensional cadmium(II) coordination polymers generated from polydentate Schiff-base ligand
- (2012) Yan Bai et al. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
- Achieving fast convergence of ab initio free energy perturbation calculations with the adaptive force-matching method
- (2012) Eric R. Pinnick et al. THEORETICAL CHEMISTRY ACCOUNTS
- MSCALE: A General Utility for Multiscale Modeling
- (2011) H. Lee Woodcock et al. Journal of Chemical Theory and Computation
- Approaching post-Hartree–Fock quality potential energy surfaces with simple pair-wise expressions: parameterising point-charge-based force fields for liquid water using the adaptive force matching method
- (2011) Feng Wang et al. MOLECULAR SIMULATION
- Communication: Hybrid ensembles for improved force matching
- (2010) Lee-Ping Wang et al. JOURNAL OF CHEMICAL PHYSICS
- The quest for the best nonpolarizable water model from the adaptive force matching method
- (2010) Omololu Akin-Ojo et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- The SAMPL2 blind prediction challenge: introduction and overview
- (2010) Matthew T. Geballe et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Good Practices in Free-Energy Calculations
- (2010) Andrew Pohorille et al. JOURNAL OF PHYSICAL CHEMISTRY B
- 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
- Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method
- (2008) Omololu Akin-Ojo et al. JOURNAL OF CHEMICAL PHYSICS
- Statistically optimal analysis of samples from multiple equilibrium states
- (2008) Michael R. Shirts et al. JOURNAL OF CHEMICAL PHYSICS
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started