Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation
出版年份 2021 全文链接
标题
Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation
作者
关键词
-
出版物
Scientific Reports
Volume 11, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2021-01-13
DOI
10.1038/s41598-020-80769-1
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Advances in the calculation of binding free energies
- (2020) Anita de Ruiter et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Rigorous Free Energy Simulations in Virtual Screening
- (2020) Zoe Cournia et al. Journal of Chemical Information and Modeling
- Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects
- (2020) Christina E. M. Schindler et al. Journal of Chemical Information and Modeling
- Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo
- (2020) Teresa Danielle Bergazin et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking
- (2019) Jeffrey R. Wagner et al. STRUCTURE
- Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability
- (2019) Qingyi Yang et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations
- (2018) Haohao Fu et al. Journal of Chemical Information and Modeling
- AMG 176, a Selective MCL1 Inhibitor, is Effective in Hematological Cancer Models Alone and in Combination with Established Therapies
- (2018) Sean Caenepeel et al. Cancer Discovery
- Absolute binding free energies for the SAMPL6 cucurbit[8]uril host–guest challenge via the AMOEBA polarizable force field
- (2018) Marie L. Laury et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
- (2017) Zoe Cournia et al. Journal of Chemical Information and Modeling
- New Coarse Variables for the Accurate Determination of Standard Binding Free Energies
- (2017) Haohao Fu et al. Journal of Chemical Theory and Computation
- Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain
- (2017) Germano Heinzelmann et al. Journal of Chemical Theory and Computation
- Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration
- (2017) Tai-Sung Lee et al. Journal of Chemical Theory and Computation
- Fragment-Based, Structure-Enabled Discovery of Novel Pyridones and Pyridone Macrocycles as Potent Bromodomain and Extra-Terminal Domain (BET) Family Bromodomain Inhibitors
- (2017) Le Wang et al. JOURNAL OF MEDICINAL CHEMISTRY
- Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations
- (2017) Matteo Aldeghi et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
- (2017) Peter Eastman et al. PLoS Computational Biology
- Advances in free-energy-based simulations of protein folding and ligand binding
- (2016) Alberto Perez et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Unconstrained enhanced sampling for free energy calculations of biomolecules: a review
- (2016) Yinglong Miao et al. MOLECULAR SIMULATION
- Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field
- (2016) David R. Bell et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Accurate calculation of the absolute free energy of binding for drug molecules
- (2016) Matteo Aldeghi et al. Chemical Science
- Accurate Binding Free Energy Predictions in Fragment Optimization
- (2015) Thomas B. Steinbrecher et al. Journal of Chemical Information and Modeling
- Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics
- (2015) Niel M. Henriksen et al. Journal of Chemical Theory and Computation
- Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
- (2015) Chad W. Hopkins et al. Journal of Chemical Theory and Computation
- Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
- (2015) Lingle Wang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- An Overview of Electrostatic Free Energy Computations for Solutions and Proteins
- (2014) Yen-Lin Lin et al. Journal of Chemical Theory and Computation
- Computation of Standard Binding Free Energies of Polar and Charged Ligands to the Glutamate Receptor GluA2
- (2014) Germano Heinzelmann et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Accuracy Assessment and Automation of Free Energy Calculations for Drug Design
- (2013) Clara D. Christ et al. Journal of Chemical Information and Modeling
- Separated topologies—A method for relative binding free energy calculations using orientational restraints
- (2013) Gabriel J. Rocklin et al. JOURNAL OF CHEMICAL PHYSICS
- Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects
- (2013) Gabriel J. Rocklin et al. JOURNAL OF CHEMICAL PHYSICS
- 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
- CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
- (2012) Sunhwan Jo et al. Journal of Chemical Information and Modeling
- Perspective: Alchemical free energy calculations for drug discovery
- (2012) David L. Mobley et al. JOURNAL OF CHEMICAL PHYSICS
- Discovery of Potent Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods and Structure-Based Design
- (2012) Anders Friberg et al. JOURNAL OF MEDICINAL CHEMISTRY
- Alchemical free energy methods for drug discovery: progress and challenges
- (2011) John D Chodera et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- The hidden energetics of ligand binding and activation in a glutamate receptor
- (2011) Albert Y Lau et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Open Babel: An open chemical toolbox
- (2011) Noel M O'Boyle et al. Journal of Cheminformatics
- Efficient Drug Lead Discovery and Optimization
- (2009) William L. Jorgensen ACCOUNTS OF CHEMICAL RESEARCH
- Basic ingredients of free energy calculations: A review
- (2009) Clara D. Christ et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
- (2009) Oleg Trott et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
- (2008) Yuqing Deng 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
- CHARMM-GUI: A web-based graphical user interface for CHARMM
- (2008) Sunhwan Jo et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- 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
- Calculation of protein-ligand binding free energy by using a polarizable potential
- (2008) D. Jiao et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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