Guidelines for the analysis of free energy calculations

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Journal of Computer-Aided Molecular Design

• Publication date

  2015-03-26

• Fields of study

  Chemistry, Medicine, Computer Science

• Identifiers
  DOI 10.1007/s10822-015-9840-9PMID 25808134PMCID PMC4420631
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Drug Design : Structure-and Ligand-Based Approaches

  2017cited by this paper
• Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions.

  2015cited by this paper
• Frontiers in free‐energy calculations of biological systems

  2014cited by this paper
• Converging free energies of binding in cucurbit[7]uril and octa-acid host–guest systems from SAMPL4 using expanded ensemble simulations

  2014cited by this paper
• GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

  2013cited by this paper
• Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

  2013cited by this paper
• Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein‐ligand binding free energies

  2013cited by this paper
• New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.

  2012cited by this paper
• A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods.

  2011influential reference
• Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation.

  2011cited by this paper
• Linear‐scaling soft‐core scheme for alchemical free energy calculations

  2011cited by this paper
• Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.

  2011cited by this paper
• Drug Design: STRUCTURAL BIOLOGY

  2010cited by this paper
• Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

  2010cited by this paper
• Good practices in free-energy calculations.

  2010influential reference
• Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.

  2010cited by this paper
• Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

  2009cited by this paper
• Computations of standard binding free energies with molecular dynamics simulations.

  2009cited by this paper
• Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations.

  2009cited by this paper
• Statistically optimal analysis of samples from multiple equilibrium states.

  2008influential reference
• Variance minimization of free energy estimates from optimized expanded ensembles.

  2008cited by this paper
• Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

  2007cited by this paper
• Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.

  2007cited by this paper
• From Algorithms to Applications

  2007cited by this paper
• Matplotlib: A 2D Graphics Environment

  2007cited by this paper
• In search of the hair-cell gating spring elastic properties of ankyrin and cadherin repeats.

  2005cited by this paper
• Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence.

  2004cited by this paper
• Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

  2003cited by this paper
• A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations

  2002cited by this paper
• Understanding Molecular Simulation

  2001influential reference
• Steered molecular dynamics simulations of force‐induced protein domain unfolding

  1999cited by this paper
• Mechanical unfolding intermediates in titin modules

  1999cited by this paper
• Multistate Gaussian Model for Electrostatic Solvation Free Energies

  1997cited by this paper
• Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules

  1997cited by this paper
• Understanding molecular simulation: from algorithms to applications

  1996influential reference
• Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations

  1994cited by this paper
• Free energy calculations for Lennard-Jones systems and water using the expanded ensemble method A Monte Carlo and molecular dynamics simulation study

  1994cited by this paper
• Separation‐shifted scaling, a new scaling method for Lennard‐Jones interactions in thermodynamic integration

  1994cited by this paper
• New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles

  1992cited by this paper
• Drug design

  1992cited by this paper
• THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

  1992cited by this paper
• MOLECULAR SIMULATION: Applications to Chemical and Biomolecular Systems

  1989cited by this paper
• Error estimates on averages of correlated data

  1989cited by this paper
• Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water

  1986cited by this paper
• Efficient estimation of free energy differences from Monte Carlo data

  1976influential reference
• High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

  1954cited by this paper
• Statistical Mechanics of Fluid Mixtures

  1935cited by this paper

• Weak salting-out of H2 gas from aqueous NaCl solutions confined in kaolinite nanopores

  2026cites this paper
• A Neural Time-Series Learning Method for Accelerating Free-Energy Perturbation and Rare-Event Molecular Dynamics Simulations.

  2026cites this paper
• Enhanced Diffusion Sampling: Efficient Rare Event Sampling and Free Energy Calculation with Diffusion Models

  2026influential citation
• Rare Event Analysis of Large Language Models

  2026cites this paper
• Water and chloroform pure component and binary mixtures: New insights from molecular dynamics simulations.

  2026cites this paper
• Coarse-grained molecular dynamics simulation of gallic acid delivery using span60-based niosomes

  2026cites this paper
• Impact of Varying Velocities and Solvation Boxes on Alchemical Free-Energy Simulations

  2025cites this paper
• Structural and Energetic Evidence Supports the Non-Covalent Phosphate Cyclization by the Class II Phospholipase D from Loxosceles intermedia

  2025cites this paper
• TRIM21-Driven Degradation of BRD4: Development of Heterobifunctional Degraders and Investigation of Recruitment and Selectivity Mechanisms

  2025cites this paper
• Simple Method to Optimize the Spacing and Number of Alchemical Intermediates in Expanded Ensemble Free Energy Calculations

  2025cites this paper
• FEP-SPell-ABFE: An Open-Source Automated Alchemical Absolute Binding Free-Energy Calculation Workflow for Drug Discovery

  2025cites this paper
• IMERGE-FEP: Improving Relative Free Energy Calculation Convergence with Chemical Intermediates

  2025cites this paper
• MEDOC: A Fast, Scalable, and Mathematically Exact Algorithm for the Site-Specific Prediction of the Protonation Degree in Large Disordered Proteins

  2025cites this paper
• Thermodynamics and Transport Properties of Gabapentin, Paracetamol, & Albuterol in Water

  2025cites this paper
• Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function

  2025cites this paper
• Flexibility in PAM recognition expands DNA targeting in xCas9

  2025cites this paper
• Machine-Learned Electrostatic Potentials for Accurate Hydration Free Energy Calculations

  2025cites this paper
• ALCHEMD: Bridging Accessibility and Accuracy in Automated Relative Binding Free Energy Workflows.

  2025cites this paper
• In Silico Peptide Design: Methods, Resources, and Role of AI

  2025cites this paper
• Quantitative analysis of reactive dye–cellulose affinity via molecular dynamics simulations verified by diffusion experiments

  2025cites this paper
• A free energy perturbation-assisted machine learning strategy for mimotope screening in neoantigen-based vaccine design

  2025cites this paper
• FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks

  2025cites this paper
• Active Learning FEP Using 3D-QSAR for Prioritizing Bioisosteres in Medicinal Chemistry.

  2025cites this paper
• Coarse-grained molecular dynamics simulations on self-assembly of polystyrene-block-poly(2-Vinylpyridine)

  2025cites this paper
• CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions

  2025cites this paper
• Uncovering the potential of the anchor site for enhancing Golgi alpha-mannosidase II selectivity using molecular dynamics simulations and free energy calculations

  2025cites this paper
• Effective polarization in potassium channel simulations: Ion conductance, occupancy, voltage response, and selectivity

  2025cites this paper
• Thermodynamics Properties of Leucine and Isoleucine Peptides in Water

  2025cites this paper
• Automated Workflow for Absolute Binding Free Energy Calculations with Implicit Solvent and Double Decoupling

  2025influential citation
• Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function

  2025cites this paper
• Flexibility in PAM Recognition Expands DNA Targeting in xCas9

  2025cites this paper
• Computational Elucidation of Sterol Recognition by SREBP Cleavage Activatory Protein

  2025cites this paper
• In Silico Design of High-Affinity gp100 Antigenic Mimotopes for Targeting Melanoma.

  2025cites this paper
• Modular and Interoperable Workflows for Benchmarking Alchemical Binding Free Energy Calculation Methodologies

  2025cites this paper
• Design of TCR-mimicking binders for pHLA with high potency

  2025cites this paper
• SAMTI: Sampling Adaptive Thermodynamic Integration for Alchemical Free Energy Calculations

  2025cites this paper
• Novel DNJ Derivative Ameliorates Cardiac Hypertrophy by Targeting OPA1 and Restoring Mitochondrial Health.

  2025cites this paper
• Coarse-grained representation of cucurbiturils in aqueous media within the Martini 3 force field.

  2025cites this paper
• Extending machine learning model for implicit solvation to free energy calculations

  2025cites this paper
• Unveiling Molecular Features Controlling the Solubility of Hydrofluorocarbons in Fluorine-Based Eutectic Solvents

  2025cites this paper
• Exact fluctuation relation for open systems beyond the Zwanzig FEP equation

  2025cites this paper
• Understanding Solute-Hydrotrope Aggregation in Aqueous Solutions: A Molecular Dynamics Approach.

  2025cites this paper
• Adaptive Lambda Scheduling: A Method for Computational Efficiency in Free Energy Perturbation Simulations

  2025cites this paper
• Evaluation of All-Atom and Martini 3 Coarse-Grained Force Fields from the Structural Investigation of Nitroxide Spin Probes and Their Confinement in Beta-Cyclodextrin.

  2024cites this paper
• Docking and other computing tools in drug design against SARS-CoV-2

  2024cites this paper
• Dynamic Mechanism for Subtype Selectivity of Endocannabinoids

  2024cites this paper
• Thermodynamic insights into moxifloxacin hydrochloride interactions within aqueous solutions: integrating thermophysical measurements and molecular dynamics simulations at varied temperatures

  2024influential citation
• Coarse-graining the recognition of a glycolipid by the C-type lectin Mincle receptor

  2024cites this paper
• On the Statistical Mechanics of Mass Accommodation at Liquid-Vapor Interfaces.

  2024cites this paper
• Inhibition of DEF‐p65 Interactions as a Potential Avenue to Suppress Tumor Growth in Pancreatic Cancer

  2024cites this paper
• Convergence criteria for single-step free-energy calculations: the relation between the Π bias measure and the sample variance

  2024cites this paper
• Molecular and electrostatic origins of mixed salt partitioning phenomena in uncharged poly(ethylene oxide)-based membranes

  2024cites this paper
• Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions.

  2024cites this paper
• A drug-drug co-amorphous system for highly improved solubility of breviscapine: an experimental and computational study

  2024cites this paper
• Uncertainties of predictions from temperature replica exchange simulations.

  2024cites this paper
• Solvation structure and hydrogen bond dynamics of uracil–water and thymine–water: A comparison of different force fields of uracil and thymine

  2024cites this paper
• Unveiling Liquid-Phase Exfoliation of Graphite and Boron Nitride Using Fluorescent Dyes Through Combined Experiments and Simulations.

  2024cites this paper
• Guidelines for Free-Energy Calculations Involving Charge Changes

  2024cites this paper
• Functional diversity among cardiolipin binding sites on the mitochondrial ADP/ATP carrier

  2024cites this paper
• Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization

  2024cites this paper
• Peptide Drug Design Using Alchemical Free Energy Calculation: An Application and Validation on Agonists of Ghrelin Receptor

  2024cites this paper
• Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e

  2024cites this paper
• Solubility of selected polymers in cyclohexane: comparison between Flory-Huggins interaction parameters calculated using three different molecular dynamics simulation approaches.

  2024cites this paper
• The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA

  2024cites this paper
• Analysis of metadynamics simulations by metadynminer.py

  2024cites this paper
• Application of the Linear Interaction Energy Method to Nitric Oxide Synthase Structure-Based Inhibitor Design

  2024cites this paper
• MEDOC: A fast, scalable and mathematically exact algorithm for the site-specific prediction of the protonation degree in large disordered proteins

  2024cites this paper
• alchemlyb: the simple alchemistry library

  2024cites this paper
• Multiparameter Method for Developer Screening of Molecular Glass Resists via Molecular Simulations.

  2024cites this paper
• Convergence-Adaptive Roundtrip Method Enables Rapid and Accurate FEP Calculations.

  2024cites this paper
• In silico design of high-affinity antigenic peptides for HLA-B44.

  2024cites this paper
• Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations

  2024cites this paper
• A fully human IgG1 antibody targeting connexin 32 extracellular domain blocks CMTX1 hemichannel dysfunction in an in vitro model

  2024cites this paper
• RED-E-Function-Based Equilibrium Parameter Finder: Finding the Best Restraint Parameters in Absolute Binding Free Energy Calculations.

  2024cites this paper
• How Solvation Alters the Thermodynamics of Asymmetric Bond-Breaking: Quantum Simulation of NaK+ in Liquid Tetrahydrofuran

  2024influential citation
• Molecular Interactions of Perfluorinated and Branched Fluorine-Free Surfactants at Interfaces: Insights from a New Reliable Force Field.

  2024cites this paper
• Martini 3 Coarse-Grained Models of the niosomes based on Span60 and Tween60

  2024cites this paper
• The sequence-dependent morphology of self-assembly peptides after binding with organophosphorus nerve agent VX

  2024cites this paper
• Identification of novel LRRK2 inhibitors by structure-based virtual screening and alchemical free energy calculation.

  2024cites this paper
• Automated Adaptive Absolute Binding Free Energy Calculations

  2024cites this paper
• Advanced sampling simulations of coupled folding and binding of phage P22 N-peptide to boxB RNA

  2024cites this paper
• Coarse-Grained Molecular Dynamics Simulation of Heterogeneous Polysorbate 80 Surfactants and their Interactions with Small Molecules and Proteins.

  2024cites this paper
• Influence of Iodine Merz–Singh–Kollman Radius on the Calculated Charges and Hydration Free Energies of Iodinated Molecules

  2024cites this paper
• Calculated hydration free energies become less accurate with increases in molecular weight

  2024cites this paper
• Cyclopamine modulates smoothened receptor activity in a binding position dependent manner

  2024influential citation
• A Critical Look at Density Functional Theory in Chemistry: Untangling Its Strengths and Weaknesses

  2024cites this paper
• The Energetics and Ion Coupling of Cholesterol Transport Through Patched1

  2023cites this paper
• Thermodynamics and Transport Properties of Valine and Cysteine Peptides in Water

  2023cites this paper
• The reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question

  2023cites this paper
• Molecular Thermodynamic Origin of Substrate Promiscuity in the Enzyme Laccase: Toward a Broad-Spectrum Degrader of Dye Effluents.

  2023cites this paper
• Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant

  2023cites this paper
• Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes I: In Silico Implementation for Surfactant Micelles.

  2023cites this paper
• MemCross: Accelerated Weight Histogram method to assess membrane permeability.

  2023cites this paper
• DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain specific PKMζ.

  2023cites this paper
• Computational Assessment of an Amine-Based Solvent Library for High-Salinity Brine Desalination

  2023cites this paper
• Prevalence and mechanism of synergistic carboxylate-cation-water interactions in halophilic proteins

  2023cites this paper
• On the validity of some equilibrium models for thermodiffusion

  2023cites this paper
• OGRe: Optimal Grid Refinement Protocol for Accurate Free Energy Surfaces and Its Application in Proton Hopping in Zeolites and 2D COF Stacking

  2023cites this paper
• Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison

  2023influential citation
• Structural and thermodynamic framework for PIEZO1 modulation by small molecules

  2023cites this paper