Reformulating the entropic contribution in molecular docking scoring functions

II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands

(2016) Francesca Nerattini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

Virtual Screening Strategies in Drug Discovery: A Critical Review

(2013) A. Lavecchia et al.   CURRENT MEDICINAL CHEMISTRY

The Precise Chemical–Physical Nature of the Pharmacore in FK506 Binding Protein Inhibition: ElteX, a New Class of Nanomolar FKBP12 Ligands

(2013) Maria Raffaella Martina et al.   JOURNAL OF MEDICINAL CHEMISTRY

MM/GBSA Binding Energy Prediction on the PDBbind Data Set: Successes, Failures, and Directions for Further Improvement

(2012) Paulette A. Greenidge et al.   Journal of Chemical Information and Modeling

Diagnosing the decline in pharmaceutical R&D efficiency

(2012) Jack W. Scannell et al.   NATURE REVIEWS DRUG DISCOVERY

Alchemical free energy methods for drug discovery: progress and challenges

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

Advances in all atom sampling methods for modeling protein–ligand binding affinities

(2011) Emilio Gallicchio et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Intraligand Hydrophobic Interactions Rationalize Drug Affinities for Peptidyl−Prolyl Cis−Trans Isomerase Protein

(2011) Marco Bizzarri et al.   JOURNAL OF PHYSICAL CHEMISTRY B

New Perspective on How and Why Immunophilin FK506-Related Ligands Work

(2011) Marco Bizzarri et al.   Journal of Physical Chemistry Letters

Accounting for Ligand Conformational Restriction in Calculations of Protein-Ligand Binding Affinities

(2010) Cen Gao et al.   BIOPHYSICAL JOURNAL

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

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

MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening

(2009) Nicolas Sauton et al.   BMC BIOINFORMATICS

Theory of Free Energy and Entropy in Noncovalent Binding

(2009) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Importance of Ligand Reorganization Free Energy in Protein−Ligand Binding-Affinity Prediction

(2009) Chao-Yie Yang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY