Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges

Discovery of biaryls as RORγ inverse agonists by using structure-based design

(2016) Istvan J. Enyedy et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge

(2016) Zhaofeng Ye et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

(2016) Nanjie Deng et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

(2016) Majda Misini Ignjatović 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

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

(2015) Richard D. Smith et al.   Journal of Chemical Information and Modeling

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

A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool

(2015) David Ryan Koes et al.   PLoS One

A reversed sulfonamide series of selective RORc inverse agonists

(2014) Monique B. van Niel et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering

(2014) Daniel J. Cole et al.   Journal of Chemical Theory and Computation

Discovery of Selective 4-Amino-pyridopyrimidine Inhibitors of MAP4K4 Using Fragment-Based Lead Identification and Optimization

(2014) Terry D. Crawford et al.   JOURNAL OF MEDICINAL CHEMISTRY

Minor Structural Change to Tertiary Sulfonamide RORc Ligands Led to Opposite Mechanisms of Action

(2014) Olivier René et al.   ACS Medicinal Chemistry Letters

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

Chemistry and Biology Of Multicomponent Reactions

(2012) Alexander Dömling et al.   CHEMICAL REVIEWS

On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds

(2012) Michal Kolář et al.   Journal of Chemical Theory and Computation

ZINCPharmer: pharmacophore search of the ZINC database

(2012) D. R. Koes et al.   NUCLEIC ACIDS RESEARCH

Enabling Large-Scale Design, Synthesis and Validation of Small Molecule Protein-Protein Antagonists

(2012) David Koes et al.   PLoS One

Conformationally constrained farnesoid X receptor (FXR) agonists: Alternative replacements of the stilbene

(2011) Adwoa Akwabi-Ameyaw et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties

(2011) Hans G.F. Richter et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

(2011) Richard D. Smith et al.   Journal of Chemical Information and Modeling

Open3DALIGN: an open-source software aimed at unsupervised ligand alignment

(2011) Paolo Tosco et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Optimization of minimum set of protein–DNA interactions: a quasi exact solution with minimum over-fitting

(2009) N. A. Temiz et al.   BIOINFORMATICS

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Experimentally based contact energies decode interactions responsible for protein–DNA affinity and the role of molecular waters at the binding interface

(2009) N. Alpay Temiz et al.   NUCLEIC ACIDS RESEARCH