Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches
出版年份 2022 全文链接
标题
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches
作者
关键词
-
出版物
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume -, Issue -, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2022-05-22
DOI
10.1007/s10822-022-00443-8
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。- Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package
- (2021) Evgeny Epifanovsky et al. JOURNAL OF CHEMICAL PHYSICS
- Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge
- (2020) Andreas Krämer et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Psi4 1.4: Open-source software for high-throughput quantum chemistry
- (2020) Daniel G. A. Smith et al. JOURNAL OF CHEMICAL PHYSICS
- Membrane permeability of small molecules from unbiased molecular dynamics simulations
- (2020) Andreas Krämer et al. JOURNAL OF CHEMICAL PHYSICS
- GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions
- (2019) Christoph Bannwarth et al. Journal of Chemical Theory and Computation
- Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods
- (2019) Timothy J. Giese et al. Journal of Chemical Theory and Computation
- Prediction of CB[8] host–guest binding free energies in SAMPL6 using the double-decoupling method
- (2018) Kyungreem Han et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods
- (2018) Octav Caldararu et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching
- (2018) Phillip S. Hudson et al. Journal of Chemical Theory and Computation
- Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale
- (2018) Phillip S. Hudson et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Overview of the SAMPL6 host–guest binding affinity prediction challenge
- (2018) Andrea Rizzi et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
- (2017) Minkyung Baek et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- 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
- OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
- (2017) Peter Eastman et al. PLoS Computational Biology
- Overview of the SAMPL5 host–guest challenge: Are we doing better?
- (2016) Jian Yin et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge
- (2016) Juyong Lee et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Convergence of single-step free energy perturbation
- (2016) Stefan Boresch et al. MOLECULAR PHYSICS
- Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching
- (2015) Jicun Li et al. JOURNAL OF CHEMICAL PHYSICS
- Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method
- (2015) Gerhard König et al. Journal of Chemical Theory and Computation
- 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
- Computational scheme for pH-dependent binding free energy calculation with explicit solvent
- (2015) Juyong Lee et al. PROTEIN SCIENCE
- 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
- The SAMPL4 host–guest blind prediction challenge: an overview
- (2014) Hari S. Muddana et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- GalaxyDock2: Protein-ligand docking using beta-complex and global optimization
- (2013) Woong-Hee Shin et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- 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
- Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases
- (2012) Aleksandr V. Marenich 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
- Blind prediction of host–guest binding affinities: a new SAMPL3 challenge
- (2012) Hari S. Muddana et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- 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
- Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
- (2011) Jan Řezáč 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
- Current Status of the AMOEBA Polarizable Force Field
- (2010) Jay W. Ponder 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
- A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview
- (2009) J. Peter Guthrie JOURNAL OF PHYSICAL CHEMISTRY B
- 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
- Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections
- (2008) Jeng-Da Chai et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationPublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More