Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2

QSAR Model of Unbound Brain-to-Plasma Partition Coefficient, Kp,uu,brain: Incorporating P-glycoprotein Efflux as a Variable

(2016) Elena Dolgikh et al.   Journal of Chemical Information and Modeling

Prediction of Protein–Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations

(2016) Anthony J. Clark et al.   Journal of Chemical Theory and Computation

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

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

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

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization

(2015) Cen Gao et al.   Journal of Chemical Information and Modeling

Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment

(2015) Matthew P. Baumgartner 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

Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms

(2014) Andrea Cavalli et al.   ACCOUNTS OF CHEMICAL RESEARCH

Farnesoid X receptor: a master regulator of hepatic triglyceride and glucose homeostasis

(2014) Yang Jiao et al.   ACTA PHARMACOLOGICA SINICA

Protein–Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials

(2014) Manuel P. Luitz et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

(2013) Kelly L. Damm-Ganamet et al.   Journal of Chemical Information and Modeling

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

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

(2013) Kai Wang et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

QSAR Modeling: Where Have You Been? Where Are You Going To?

(2013) Artem Cherkasov et al.   JOURNAL OF MEDICINAL CHEMISTRY

Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols

(2012) David J. Osguthorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

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

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

Pharmer: Efficient and Exact Pharmacophore Search

(2011) David Ryan Koes et al.   Journal of Chemical Information and Modeling

Discovery of novel and orally active FXR agonists for the potential treatment of dyslipidemia & diabetes

(2010) Hans G.F. Richter et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers

(2010) K. Shawn Watts et al.   Journal of Chemical Information and Modeling

Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors

(2010) Francesco Colizzi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Best Practices for QSAR Model Development, Validation, and Exploitation

(2010) Alexander Tropsha   Molecular Informatics

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Exploring Complex Protein−Ligand Recognition Mechanisms with Coarse Metadynamics

(2009) Matteo Masetti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformationally constrained farnesoid X receptor (FXR) agonists: Naphthoic acid-based analogs of GW 4064

(2008) Adwoa Akwabi-Ameyaw et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

Molecule-pharmacophore superpositioning and pattern matching in computational drug design

(2007) G WOLBER   DRUG DISCOVERY TODAY