Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4

D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

(2019) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Optimized Lennard-Jones Parameters for Druglike Small Molecules

(2018) Eliot Boulanger 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

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

(2017) Tai-Sung Lee et al.   Journal of Chemical Theory and Computation

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

BACE-1 Inhibitors: From Recent Single-Target Molecules to Multitarget Compounds for Alzheimer’s Disease

(2017) Federica Prati et al.   JOURNAL OF MEDICINAL CHEMISTRY

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

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

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

(2015) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

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

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

(2014) Nadine Homeyer 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

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

(2011) Thomas Steinbrecher et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discovery and SAR of novel pyrazole-based thioethers as cathepsin S inhibitors. Part 2: Modification of P3, P4, and P5 regions

(2010) John J.M. Wiener et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Diazinones as P2 replacements for pyrazole-based cathepsin S inhibitors

(2010) Michael K. Ameriks et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Thioether acetamides as P3 binding elements for tetrahydropyrido-pyrazole cathepsin S inhibitors

(2010) Danielle K. Wiener et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Macrocyclic peptidomimetic β-secretase (BACE-1) inhibitors with activity in vivo

(2009) Rainer Machauer et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements

(2009) Michael K. Ameriks et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

λ-Dynamics free energy simulation methods

(2009) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The  -Secretase Enzyme BACE in Health and Alzheimer's Disease: Regulation, Cell Biology, Function, and Therapeutic Potential

(2009) R. Vassar et al.   JOURNAL OF NEUROSCIENCE