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

Type II Kinase Inhibitors Show an Unexpected Inhibition Mode against Parkinson’s Disease-Linked LRRK2 Mutant G2019S

(2013) Min Liu et al.   BIOCHEMISTRY

Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering

(2012) David J. Osguthorpe et al.   Chemical Biology & Drug Design

Virtual Target Screening: Validation Using Kinase Inhibitors

(2012) Daniel N. Santiago et al.   Journal of Chemical Information and Modeling

Numerical Errors and Chaotic Behavior in Docking Simulations

(2012) Miklos Feher et al.   Journal of Chemical Information and Modeling

Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines

(2012) Thijs Beuming et al.   Journal of Chemical Information and Modeling

Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure–Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis

(2012) Falgun Shah et al.   Journal of Chemical Information and Modeling

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

(2012) Matthew P. Repasky et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors

(2012) Ori Kalid et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Rational Approaches to Improving Selectivity in Drug Design

(2012) David J. Huggins 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

Novel Inverse Binding Mode of Indirubin Derivatives Yields Improved Selectivity for DYRK Kinases

(2012) Vassilios Myrianthopoulos et al.   ACS Medicinal Chemistry Letters

Contribution of Explicit Solvent Effects to the Binding Affinity of Small-Molecule Inhibitors in Blood Coagulation Factor Serine Proteases

(2011) Robert Abel et al.   ChemMedChem

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

(2011) Thijs Beuming et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Role of Water Molecules in Computational Drug Design

(2010) Stephanie de Beer et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations

(2010) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Structure-Based Discovery of Novel Chemotypes for Adenosine A2AReceptor Antagonists

(2010) Vsevolod Katritch et al.   JOURNAL OF MEDICINAL CHEMISTRY

Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs

(2009) Christopher R. Corbeil et al.   Journal of Chemical Information and Modeling

Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis

(2009) Noeris K. Salam 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

Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6

(2009) Rita Santos et al.   Journal of Chemical Information and Modeling

Identification of Novel Falcipain-2 Inhibitors as Potential Antimalarial Agents through Structure-Based Virtual Screening

(2009) Honglin Li et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of the catechol structural moiety as a Stat3 SH2 domain inhibitor by virtual screening

(2008) Wenshan Hao et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Lead Finder: An Approach To Improve Accuracy of Protein−Ligand Docking, Binding Energy Estimation, and Virtual Screening

(2008) Oleg V. Stroganov et al.   Journal of Chemical Information and Modeling

Improving database enrichment through ensemble docking

(2008) Shashidhar Rao et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

What do we know and when do we know it?

(2008) Anthony Nicholls   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Exploiting Ordered Waters in Molecular Docking

(2008) Niu Huang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Docking Study Yields Four Novel Inhibitors of the Protooncogene Pim-1 Kinase†

(2008) Albert C. Pierce et al.   JOURNAL OF MEDICINAL CHEMISTRY

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

(2008) Alan P. Graves et al.   JOURNAL OF MOLECULAR BIOLOGY

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY