The slow but steady rise of binding free energy calculations in drug discovery

Optimization of 2-Amino-4,6-diarylpyrimidine-5-carbonitriles as Potent and Selective A1 Antagonists

(2022) Cristina Val et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of MK-1454: A Potent Cyclic Dinucleotide Stimulator of Interferon Genes Agonist for the Treatment of Cancer

(2022) Wonsuk Chang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Characterizing Receptor Flexibility to Predict Mutations That Lead to Human Adaptation of Influenza Hemagglutinin

(2022) Huafeng Xu et al.   Journal of Chemical Theory and Computation

A fourth-generation high-dimensional neural network potential with accurate electrostatics including non-local charge transfer

(2021) Tsz Wai Ko et al.   Nature Communications

Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints

(2021) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series

(2021) Michael J. Palmer et al.   JOURNAL OF MEDICINAL CHEMISTRY

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

(2021) Junjie Zou et al.   Journal of Chemical Theory and Computation

Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

(2021) Si Zhang et al.   Journal of Chemical Theory and Computation

Discovery of TDI-10229: A Potent and Orally Bioavailable Inhibitor of Soluble Adenylyl Cyclase (sAC, ADCY10)

(2021) Makoto Fushimi et al.   ACS Medicinal Chemistry Letters

Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency

(2021) Chun-Hui Zhang et al.   ACS Medicinal Chemistry Letters

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

(2021) Anders S. Christensen et al.   JOURNAL OF CHEMICAL PHYSICS

Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units

(2021) Ido Y. Ben-Shalom et al.   Journal of Chemical Theory and Computation

Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences

(2021) Pengfei Li et al.   Journal of Chemical Theory and Computation

FCX‐146, a potent allosteric inhibitor of Akt kinase in cancer cells: Lead optimization of the second‐generation arylidene indanone scaffold

(2020) Meenakshisundaram Balasubramaniam et al.   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

Discovery of new AKT1 inhibitors by combination of in silico structure based virtual screening approaches and biological evaluations

(2020) Filip Fratev et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Design, Synthesis and Evaluation of Carbamate–linked Uridyl-based Inhibitors of Human ST6Gal I

(2020) Andrew P. Montgomery et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Assessment of Binding Affinity via Alchemical Free Energy Calculations

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

Discovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with In Vivo Antitumor Activity

(2020) Paul R. Leger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

(2020) Junjie Zou et al.   Journal of Chemical Information and Modeling

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

(2020) Tai-Sung Lee et al.   Journal of Chemical Theory and Computation

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

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo

(2020) Teresa Danielle Bergazin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs

(2020) Zhe Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accounting for the Central Role of Interfacial Water in Protein–Ligand Binding Free Energy Calculations

(2020) Ido Y. Ben-Shalom et al.   Journal of Chemical Theory and Computation

Reaction-Based Enumeration, Active Learning, and Free Energy Calculations To Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin-Dependent Kinase 2 Inhibitors

(2019) Kyle D. Konze et al.   Journal of Chemical Information and Modeling

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

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

Chemo-enzymatic synthesis of (E)-2,3-diaryl-5-styryl-trans-2,3-dihydrobenzofuran-based scaffolds and their in vitro and in silico evaluation as a novel sub-family of potential allosteric modulators of the 90 kDa heat shock protein (Hsp90)

(2018) Ivan Bassanini et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

(2018) Rafael Gómez-Bombarelli et al.   ACS Central Science

Computer-aided drug discovery of Myc-Max inhibitors as potential therapeutics for prostate cancer

(2018) Lavinia A. Carabet et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys

(2018) Haohao Fu et al.   Journal of Physical Chemistry Letters

Deep reinforcement learning for de novo drug design

(2018) Mariya Popova et al.   Science Advances

Discovery and Evaluation of Anti-Fibrinolytic Plasmin Inhibitors Derived from 5-(4-Piperidyl)isoxazol-3-ol (4-PIOL)

(2017) Thomas C. Schmidt et al.   Journal of Chemical Information and Modeling

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations

(2017) Albert C. Pan et al.   Journal of Chemical Theory and Computation

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost

(2017) J. S. Smith et al.   Chemical Science

Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks

(2017) Marwin H. S. Segler et al.   ACS Central Science

The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors

(2016) Mitsugu Araki et al.   Journal of Chemical Information and Modeling

Application of Free Energy Perturbation for the Design of BACE1 Inhibitors

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

A Simple Method for Automated Equilibration Detection in Molecular Simulations

(2016) John D. Chodera   Journal of Chemical Theory and Computation

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

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

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

(2016) Bradley Sherborne et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2015) Frank Lovering et al.   ChemMedChem

Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?

(2015) Shuai Liu et al.   Journal of Chemical Information and Modeling

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

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Design, Synthesis, and Protein Crystallography of Biaryltriazoles as Potent Tautomerase Inhibitors of Macrophage Migration Inhibitory Factor

(2015) Pawel Dziedzic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Discovery of Novel Inhibitors of HIV-1 Reverse Transcriptase Through Virtual Screening of Experimental and Theoretical Ensembles

(2014) Anthony Ivetac et al.   Chemical Biology & Drug Design

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

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

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

Lead optimization mapper: automating free energy calculations for lead optimization

(2013) Shuai Liu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

(2013) Robert A. Pearlstein et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies

(2011) Morgan Lawrenz 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

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

Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

(2009) Julien Michel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations

(2009) Daniel K. Shenfeld et al.   PHYSICAL REVIEW E

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS