Calculate protein–ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3

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

The Future of Cysteine Cathepsins in Disease Management

(2017) Lovro Kramer et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

(2016) Yuan Hu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

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

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

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder 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

Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation

(2015) Luigi Capoferri et al.   PLoS One

Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

(2014) C. Ruben Vosmeer et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Pyrazole-based arylalkyne Cathepsin S inhibitors. Part III: Modification of P4 region

(2012) John J.M. Wiener et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

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

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

Cysteine cathepsins: From structure, function and regulation to new frontiers

(2011) Vito Turk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

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

Recent Advances in the Design of Cathepsin S Inhibitors

(2010) John J. M. Wiener et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

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

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

(2010) James Luccarelli et al.   Journal of Chemical Theory and Computation

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

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

Pyrazole-based arylalkyne cathepsin S inhibitors. Part II: Optimization of cellular potency

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

Cysteine cathepsin S as an immunomodulatory target: present and future trends

(2008) Suman Gupta et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Discovery of Novel Cathepsin S Inhibitors by Pharmacophore-Based Virtual High-Throughput Screening

(2008) Patrick Markt et al.   Journal of Chemical Information and Modeling