To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough

Quantum-state estimation problem via optimal design of experiments

(2021) Jun Suzuki   INTERNATIONAL JOURNAL OF QUANTUM INFORMATION

Structure-Based Approaches to Improving Selectivity through Utilizing Explicit Water Molecules: Discovery of Selective β-Secretase (BACE1) Inhibitors over BACE2

(2021) Kazuki Fujimoto et al.   JOURNAL OF MEDICINAL CHEMISTRY

Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling

(2021) Gerhard König et al.   Journal of Chemical Theory and Computation

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

(2021) Junjie Zou 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

Evaluation of a Series of β-Secretase 1 Inhibitors Containing Novel Heteroaryl-Fused-Piperazine Amidine Warheads

(2019) Daniel Oehlrich et al.   ACS Medicinal Chemistry Letters

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

Eigen-Optimization on Large Graphs by Edge Manipulation

(2016) Chen Chen et al.   ACM Transactions on Knowledge Discovery from Data

Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?

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

1,4-Oxazine β-Secretase 1 (BACE1) Inhibitors: From Hit Generation to Orally Bioavailable Brain Penetrant Leads

(2015) Frederik J. R. Rombouts 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

From Angular Manifolds to the Integer Lattice: Guaranteed Orientation Estimation With Application to Pose Graph Optimization

(2014) Luca Carlone et al.   IEEE Transactions on Robotics

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

Lead optimization mapper: automating free energy calculations for lead optimization

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

Perspective: Alchemical free energy calculations for drug discovery

(2012) David L. Mobley et al.   JOURNAL OF CHEMICAL PHYSICS

Rational design and synthesis of aminopiperazinones as β-secretase (BACE) inhibitors

(2011) Gary Tresadern et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Avoiding the van der Waals endpoint problem using serial atomic insertion

(2011) Stefan Boresch et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Use and abuse of the Fisher information matrix in the assessment of gravitational-wave parameter-estimation prospects

(2008) Michele Vallisneri   PHYSICAL REVIEW D