Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics
Authors
Keywords
-
Journal
CURRENT OPINION IN STRUCTURAL BIOLOGY
Volume 67, Issue -, Pages 127-134
Publisher
Elsevier BV
Online
2020-11-19
DOI
10.1016/j.sbi.2020.08.001
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Overcoming Orthogonal Barriers in Alchemical Free Energy Calculations: On the Relative Merits of λ-Variations, λ-Extrapolations, and Biasing
- (2020) David F. Hahn et al. Journal of Chemical Theory and Computation
- The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations
- (2020) Andrea Rizzi et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Assessment of Binding Affinity via Alchemical Free Energy Calculations
- (2020) Maximilian Kuhn et al. Journal of Chemical Information and Modeling
- Rigorous Free Energy Simulations in Virtual Screening
- (2020) Zoe Cournia et al. Journal of Chemical Information and Modeling
- Crowdsourcing drug discovery for pandemics
- (2020) John Chodera et al. Nature Chemistry
- Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques
- (2019) Petra Rovó et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Using AMBER18 for Relative Free Energy Calculations
- (2019) Lin Frank Song et al. Journal of Chemical Information and Modeling
- Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations
- (2019) Rajat K. Pal et al. JOURNAL OF CHEMICAL PHYSICS
- Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates
- (2019) Piero Procacci JOURNAL OF CHEMICAL PHYSICS
- Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches
- (2019) Piero Procacci JOURNAL OF CHEMICAL PHYSICS
- GRAM: A True Null Model for Relative Binding Affinity Predictions
- (2019) Guanglei Cui et al. Journal of Chemical Information and Modeling
- Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models
- (2018) Haiyang Zhang et al. Journal of Chemical Information and Modeling
- Myeloid Cell Leukemia 1 Inhibition: An in Silico Study Using Non-equilibrium Fast Double Annihilation Technology
- (2018) Piero Procacci Journal of Chemical Theory and Computation
- Uncertainty Quantification in Alchemical Free Energy Methods
- (2018) Agastya P. Bhati et al. Journal of Chemical Theory and Computation
- Assessing the stability of free-energy perturbation calculations by performing variations in the method
- (2018) Francesco Manzoni et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- SAMPL6 host–guest blind predictions using a non equilibrium alchemical approach
- (2018) Piero Procacci et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Statistical efficiency of methods for computing free energy of hydration
- (2018) Ahmet Yildirim et al. JOURNAL OF CHEMICAL PHYSICS
- Escaping Atom Types in Force Fields Using Direct Chemical Perception
- (2018) David L. Mobley et al. Journal of Chemical Theory and Computation
- Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas
- (2018) Bernhard Knapp et al. Journal of Chemical Theory and Computation
- Overview of the SAMPL6 host–guest binding affinity prediction challenge
- (2018) Andrea Rizzi et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation
- (2018) Matteo Aldeghi et al. ACS Central Science
- pmx Webserver: A User Friendly Interface for Alchemistry
- (2017) Vytautas Gapsys et al. Journal of Chemical Information and Modeling
- Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories
- (2017) Piero Procacci et al. Journal of Chemical Theory and Computation
- BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation
- (2017) Zhao X. Sun et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration
- (2016) Agastya P. Bhati et al. Journal of Chemical Theory and Computation
- On the calculation of equilibrium thermodynamic properties from molecular dynamics
- (2016) Peter V. Coveney et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- I. Dissociation free energies of drug–receptor systems via non-equilibrium alchemical simulations: a theoretical framework
- (2016) Piero Procacci PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands
- (2016) Francesca Nerattini et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures
- (2015) Piero Procacci JOURNAL OF CHEMICAL PHYSICS
- Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics
- (2015) Niel M. Henriksen et al. Journal of Chemical Theory and Computation
- Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions
- (2015) Levi N. Naden et al. Journal of Chemical Theory and Computation
- OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins
- (2015) Edward Harder et al. Journal of Chemical Theory and Computation
- Computational Study of the “DFG-Flip” Conformational Transition in c-Abl and c-Src Tyrosine Kinases
- (2015) Yilin Meng et al. JOURNAL OF PHYSICAL CHEMISTRY B
- 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
- Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors
- (2013) Lingle Wang 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
- Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
- (2011) Carl Caleman et al. Journal of Chemical Theory and Computation
- Let’s get honest about sampling
- (2011) David L. Mobley JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
- (2010) Wei Jiang et al. Journal of Chemical Theory and Computation
- Good Practices in Free-Energy Calculations
- (2010) Andrew Pohorille et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Theory of Free Energy and Entropy in Noncovalent Binding
- (2009) Huan-Xiang Zhou et al. CHEMICAL REVIEWS
- Statistically optimal analysis of samples from multiple equilibrium states
- (2008) Michael R. Shirts et al. JOURNAL OF CHEMICAL PHYSICS
Publish 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 MoreCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now