D. L. Mobley

POPSHIFT: A THERMODYNAMICALLY SOUND APPROACH TO ESTIMATE BINDING FREE ENERGIES BY ACCOUNTING FOR LIGAND-INDUCED POPULATION SHIFTS FROM A LIGAND-FREE MSM

The paper introduces PopShift, a method to estimate binding free energies by accounting for ligand-induced population shifts in protein conformations using Markov state models, showing improved accuracy over traditional methods.

Molecular-Dynamics Simulation Methods for Macromolecular Crystallography

The paper applies molecular-dynamics simulations to macromolecular crystallography to refine protein structures and improve interpretation of electron density.

Capturing non-local through-bond effects in molecular mechanics force fields: II. Using fractional bond orders to fit torsion parameters

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques

The paper compares MD simulation techniques for rehydrating buried water sites in protein-ligand binding, finding that grand outperforms BLUES and normal MD, but water sampling remains challenging.

Overview of the SAMPL6 pKa Challenge: Evaluating small molecule microscopic and macroscopic pKa predictions

The paper evaluates pKa prediction methods for drug-like molecules, finding that top submissions achieved RMSE of 0.7-1.0 pKa units, but significant inaccuracies remain, especially for sulfur-containing heterocycles and multiprotic molecules.

Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans

The paper introduces a method to assess and improve fragmentation schemes for quantum chemical torsion scans by using fractional Wiberg bond orders to preserve chemical environment accuracy.

Structural and molecular dynamics of Mycobacterium tuberculosis malic enzyme, a potential anti-TB drug target

This study presents the X-ray structure of Mtb malic enzyme and uses MD simulations to reveal its dynamic behavior, informing potential inhibitor design.

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge

This paper evaluates the accuracy of octanol-water partition coefficient predictions in the SAMPL6 log P Challenge, finding improved performance compared to previous challenges and highlighting the effectiveness of various methods.

The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

This study evaluates binding free energy calculation methods using the SAMPL6 challenge, finding variations in efficiency and reproducibility across different systems and methods.

Octanol-water partition coefficient measurements for the SAMPL6 Blind Prediction Challenge

This paper presents a dataset of octanol-water log P values for 11 compounds from the SAMPL6 Part II Partition Coefficient Challenge and describes the experimental protocol used to measure them.

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

This study uses MD simulations of a crystalline protein to analyze collective motions, finding liquid-like motions dominate inter-protein dynamics while rigid-body motions are present but subsumed within the overall liquid-like behavior.

The structure of Mycobacterium tuberculosis heme-degrading protein, MhuD, in complex with product

This study determines the structure of MhuD-R26S in complex with biliverdin IX, revealing two BV molecules per active site and a new helix, suggesting a need for a protein to extract the product.

Overview of the SAMPL6 host-guest binding affinity prediction challenge

This paper provides an overview of the SAMPL6 host-guest binding affinity prediction challenge, highlighting methodological improvements and remaining challenges in predicting binding affinities.

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

The paper evaluates pKa prediction methods using a dataset of kinase inhibitor-like fragments measured by UV absorbance and NMR.

Predicting binding free energies: Frontiers and benchmarks

This paper discusses challenges in binding free energy calculations and advocates for benchmark test systems to improve their reliability in drug discovery.