The maximal and current accuracy of rigorous protein-ligand binding free energy calculations

Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field

(2023) Simon Boothroyd et al.   Journal of Chemical Theory and Computation

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

(2022) Vytautas Gapsys et al.   Journal of Chemical Information and Modeling

Discovery of allosteric SHP2 inhibitors through ensemble-based consensus molecular docking, endpoint and absolute binding free energy calculations

(2022) Maryam Jama et al.   COMPUTERS IN BIOLOGY AND MEDICINE

AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA)

(2022) Abir Ganguly et al.   Journal of Chemical Information and Modeling

Free Energy Perturbation in the Design of EED Ligands as Inhibitors of Polycomb Repressive Complex 2 (PRC2) Methyltransferase

(2021) Daniel H. O' Donovan et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Predictions: New Opportunities and Challenges for Drug Discovery

(2021) Zhixiong Lin et al.   Journal of Chemical Information and Modeling

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

(2021) Yudong Qiu et al.   Journal of Chemical Theory and Computation

OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space

(2021) Chao Lu et al.   Journal of Chemical Theory and Computation

Potency- and Selectivity-Enhancing Mutations of Conotoxins for Nicotinic Acetylcholine Receptors Can Be Predicted Using Accurate Free-Energy Calculations

(2021) Dana Katz et al.   Marine Drugs

Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots

(2021) Callum J Dickson et al.   Journal of Chemical Information and Modeling

Free energy perturbation (FEP)-guided scaffold hopping

(2021) Deyan Wu et al.   Acta Pharmaceutica Sinica B

Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations

(2020) Daniel Cappel et al.   Journal of Chemical Information and Modeling

Computationally Empowered Workflow Identifies Novel Covalent Allosteric Binders for KRAS G12C

(2020) Jérémie Mortier et al.   ChemMedChem

Assessment of Binding Affinity via Alchemical Free Energy Calculations

(2020) Maximilian Kuhn et al.   Journal of Chemical Information and Modeling

Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation

(2020) Francesca Deflorian et al.   Journal of Chemical Information and Modeling

Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis

(2020) Janet L. Paulsen 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

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

(2020) Tai-Sung Lee et al.   Journal of Chemical Information and Modeling

Advancing Free-Energy Calculations of Metalloenzymes in Drug Discovery via Implementation of LFMM Potentials

(2020) Steven Dajnowicz et al.   Journal of Chemical Theory and Computation

Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo

(2020) Gregory A. Ross et al.   Journal of Chemical Theory and Computation

Application of Molecular Dynamics Simulations to the Design of Nucleotide Inhibitors Binding to Norovirus Polymerase

(2020) Holly Freedman et al.   Journal of Chemical Information and Modeling

Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics

(2020) E. Prabhu Raman et al.   Journal of Chemical Theory and Computation

3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition

(2020) María Majellaro et al.   JOURNAL OF MEDICINAL CHEMISTRY

Quantifying the Interactions between Biomolecules: Guidelines for Assay Design and Data Analysis

(2019) Peter J Tonge   ACS Infectious Diseases

QligFEP: an automated workflow for small molecule free energy calculations in Q

(2019) Willem Jespers et al.   Journal of Cheminformatics

Using AMBER18 for Relative Free Energy Calculations

(2019) Lin Frank Song et al.   Journal of Chemical Information and Modeling

Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics

(2019) Haoyu S. Yu et al.   Journal of Chemical Information and Modeling

Optimal Measurement Network of Pairwise Differences

(2019) Huafeng Xu   Journal of Chemical Information and Modeling

Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability

(2019) Qingyi Yang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

(2018) Trung Hai Nguyen et al.   PLoS One

Repeatability, precision, and accuracy of the enthalpies and Gibbs energies of a protein–ligand binding reaction measured by isothermal titration calorimetry

(2018) Vaida Paketurytė et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Comparative Assessment of Scoring Functions: The CASF-2016 Update

(2018) Minyi Su et al.   Journal of Chemical Information and Modeling

Predicting the Binding of Fatty Acid Amide Hydrolase Inhibitors by Free Energy Perturbation

(2018) Arjun Saha et al.   Journal of Chemical Theory and Computation

Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges

(2018) Wei Chen et al.   Journal of Chemical Theory and Computation

Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations

(2018) Hannah E. Bruce Macdonald et al.   Journal of Chemical Theory and Computation

Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States

(2018) César de Oliveira et al.   Journal of Chemical Theory and Computation

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study

(2017) Henrik Keränen et al.   Journal of Chemical Theory and Computation

Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets

(2017) Haoyu S. Yu et al.   Journal of Chemical Theory and Computation

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors

(2017) Bernd Kuhn et al.   JOURNAL OF MEDICINAL CHEMISTRY

Application of Free Energy Perturbation for the Design of BACE1 Inhibitors

(2016) Myriam Ciordia et al.   Journal of Chemical Information and Modeling

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

(2016) Lingle Wang et al.   Journal of Chemical Theory and Computation

Development of a Potent, Specific CDK8 Kinase Inhibitor Which Phenocopies CDK8/19 Knockout Cells

(2016) Michael F. T. Koehler et al.   ACS Medicinal Chemistry Letters

Imidazotriazines: Spleen Tyrosine Kinase (Syk) Inhibitors Identified by Free-Energy Perturbation (FEP)

(2015) Frank Lovering et al.   ChemMedChem

Accurate Binding Free Energy Predictions in Fragment Optimization

(2015) Thomas B. Steinbrecher et al.   Journal of Chemical Information and Modeling

Fragment-Based Discovery of a Small Molecule Inhibitor of Bruton’s Tyrosine Kinase

(2015) Christopher R. Smith et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

Comparability of Mixed IC50 Data – A Statistical Analysis

(2013) Tuomo Kalliokoski et al.   PLoS One

The Experimental Uncertainty of Heterogeneous Public Ki Data

(2012) Christian Kramer et al.   JOURNAL OF MEDICINAL CHEMISTRY

Systematic errors in isothermal titration calorimetry: Concentrations and baselines

(2011) Joel Tellinghuisen et al.   ANALYTICAL BIOCHEMISTRY

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

Computationally-Guided Optimization of a Docking Hit to Yield Catechol Diethers as Potent Anti-HIV Agents

(2011) Mariela Bollini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Healthy skepticism: assessing realistic model performance

(2009) Scott P. Brown et al.   DRUG DISCOVERY TODAY