Suitability of MMGBSA for the selection of correct ligand binding modes from docking results

Endocrine Disruption at the Androgen Receptor: Employing Molecular Dynamics and Docking for Improved Virtual Screening and Toxicity Prediction

(2018) Joel Wahl et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?

(2018) David Ramírez et al.   MOLECULES

Improving Docking Performance Using Negative Image-Based Rescoring

(2018) Sami T. Kurkinen et al.   Frontiers in Pharmacology

Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches

(2017) Stefano Motta et al.   Journal of Chemical Information and Modeling

Investigation of the binding mode of 1, 3, 4-oxadiazole derivatives as amide-based inhibitors for soluble epoxide hydrolase (sEH) by molecular docking and MM-GBSA

(2016) Leila Karami et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles

(2016) Robert V. Swift et al.   Journal of Chemical Information and Modeling

Molecular mechanism of R-bicalutamide switching from androgen receptor antagonist to agonist induced by amino acid mutations using molecular dynamics simulations and free energy calculation

(2016) Hongli Liu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

(2016) Zhe Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

(2015) Joseph W. Kaus 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

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening

(2015) Salla I. Virtanen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Inhibitory effects and oxidation of 6-methylcoumarin, 7-methylcoumarin and 7-formylcoumarinviahuman CYP2A6 and its mouse and pig orthologous enzymes

(2015) Risto O. Juvonen et al.   XENOBIOTICA

Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes

(2015) Hannu Raunio et al.   Frontiers in Pharmacology

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

Effects of protein flexibility on the site of metabolism prediction for CYP2A6 substrates

(2014) Yayun Sheng et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Identification of a new androgen receptor (AR) co-regulator BUD31 and related peptides to suppress wild-type and mutated AR-mediated prostate cancer growth via peptide screening and X-ray structure analysis

(2014) Cheng-Lung Hsu et al.   Molecular Oncology

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Identification of the 5,5-dioxo-7,8-dihydro-6H-thiopyrano[3,2-d]pyrimidine derivatives as highly selective PDE4B inhibitors

(2013) Taiji Goto et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

MMGBSA As a Tool To Understand the Binding Affinities of Filamin–Peptide Interactions

(2013) Mikko Ylilauri et al.   Journal of Chemical Information and Modeling

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Discovery of oxazole-based PDE4 inhibitors with picomolar potency

(2012) Rongze Kuang et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Phosphodiesterase inhibitors. Part 4: Design, synthesis and structure-activity relationships of dual PDE3/4-inhibitory fused bicyclic heteroaromatic-4,4-dimethylpyrazolones

(2012) Koji Ochiai et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Phosphodiesterase inhibitors. Part 5: Hybrid PDE3/4 inhibitors as dual bronchorelaxant/anti-inflammatory agents for inhaled administration

(2012) Koji Ochiai et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes

(2012) Jed Zaretzki et al.   Journal of Chemical Information and Modeling

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations

(2012) Mehrnoosh Arrar et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

(2012) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphodiesterase inhibitors. Part 1: Synthesis and structure–activity relationships of pyrazolopyridine–pyridazinone PDE inhibitors developed from ibudilast

(2011) Robert W. Allcock et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Alchemical free energy methods for drug discovery: progress and challenges

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

Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine

(2011) Natasha M. DeVore et al.   FEBS Journal

Comparison of Virtual High-Throughput Screening Methods for the Identification of Phosphodiesterase-5 Inhibitors

(2011) Sanna P. Niinivehmas et al.   Journal of Chemical Information and Modeling

Unexpected Binding Orientation of Bulky-B-Ring Anti-Androgens and Implications for Future Drug Targets

(2011) Charles B. Duke 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

Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site

(2010) Salla I. Virtanen et al.   Journal of Chemical Information and Modeling

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Improved Replica Exchange Method for Native-State Protein Sampling

(2010) Samuel L. C. Moors et al.   Journal of Chemical Theory and Computation

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How different from random are docking predictions when ranked by scoring functions?

(2010) Elisenda Feliu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

(2009) Oliver Korb et al.   Journal of Chemical Information and Modeling

Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

(2009) Jason B. Cross et al.   Journal of Chemical Information and Modeling

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

(2009) Sarah E. Boyce et al.   JOURNAL OF MOLECULAR BIOLOGY

Rhodanine derivatives as novel inhibitors of PDE4

(2008) Mark W. Irvine et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Effect of B-ring substitution pattern on binding mode of propionamide selective androgen receptor modulators

(2008) Casey E. Bohl et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

(2008) César Augusto F. de Oliveira et al.   Journal of Chemical Theory and Computation