Integrating structure-based and ligand-based approaches for computational drug design

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Structural ensemble in computational drug screening

(2010) Yoshifumi Fukunishi   Expert Opinion on Drug Metabolism & Toxicology

Influence of Linker Geometry on Uranyl Complexation by Rigidly Linked Bis(3-hydroxy-N-methyl-pyridin-2-one)†

(2010) Géza Szigethy et al.   INORGANIC CHEMISTRY

Rationalization of the Performance and Target Dependence of Similarity Searching Incorporating Protein−Ligand Interaction Information

(2010) Lu Tan et al.   Journal of Chemical Information and Modeling

Computer-aided drug design platform using PyMOL

(2010) Markus A. Lill et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Benzimidazol-2-ylidene Gold(I) Complexes Are Thioredoxin Reductase Inhibitors with Multiple Antitumor Properties

(2010) Riccardo Rubbiani et al.   JOURNAL OF MEDICINAL CHEMISTRY

Three-Dimensional Protein-Ligand Interaction Scaling of Two-Dimensional Fingerprints

(2009) Lu Tan et al.   Chemical Biology & Drug Design

Utilizing Target-Ligand Interaction Information in Fingerprint Searching for Ligands of Related Targets

(2009) Lu Tan et al.   Chemical Biology & Drug Design

Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H4Receptor

(2009) Yusuf Tanrikulu et al.   ChemMedChem

Molecular Docking of Carbohydrate Ligands to Antibodies: Structural Validation against Crystal Structures

(2009) Mark Agostino et al.   Journal of Chemical Information and Modeling

Development and Validation of a Novel Protein−Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands

(2009) Nathanael Weill et al.   Journal of Chemical Information and Modeling

Position Specific Interaction Dependent Scoring Technique for Virtual Screening Based on Weighted Protein−Ligand Interaction Fingerprint Profiles

(2009) Ravi K. Nandigam et al.   Journal of Chemical Information and Modeling

APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening

(2009) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data

(2009) Sebastian G. Rohrer et al.   Journal of Chemical Information and Modeling

High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields

(2009) Simone Sciabola et al.   Journal of Chemical Information and Modeling

Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening

(2009) Tomohiro Sato et al.   Journal of Chemical Information and Modeling

Atom-Centered Interacting Fragments and Similarity Search Applications

(2009) José Batista et al.   Journal of Chemical Information and Modeling

Classical and 3D-QSAR studies of cytochrome 17 inhibitor imidazole-substituted biphenyls

(2009) Partha Pratim Roy et al.   MOLECULAR SIMULATION

Molecular Determinants of Juvenile Hormone Action as Revealed by 3D QSAR Analysis in Drosophila

(2009) Denisa Liszeková et al.   PLoS One

StoneHinge: Hinge prediction by network analysis of individual protein structures

(2009) Kevin S. Keating et al.   PROTEIN SCIENCE

Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR

(2009) Sean Ekins et al.   PLoS Computational Biology

Integrating Structure- and Ligand-Based Virtual Screening: Comparison of Individual, Parallel, and Fused Molecular Docking and Similarity Search Calculations on Multiple Targets

(2008) Lu Tan et al.   ChemMedChem

Mixed-Model QSAR at the Glucocorticoid Receptor: Predicting the Binding Mode and Affinity of Psychotropic Drugs

(2008) Morena Spreafico et al.   ChemMedChem

Ligand-Target Interaction-Based Weighting of Substructures for Virtual Screening

(2008) Thomas J. Crisman et al.   Journal of Chemical Information and Modeling

An Integrated Approach to Ligand- and Structure-Based Drug Design: Development and Application to a Series of Serine Protease Inhibitors

(2008) Orazio Nicolotti et al.   Journal of Chemical Information and Modeling

Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein−Ligand Interactions

(2008) Lu Tan et al.   Journal of Chemical Information and Modeling

Knowledge Based Identification of Potent Antitubercular Compounds Using Structure Based Virtual Screening and Structure Interaction Fingerprints

(2008) Ashutosh Kumar et al.   Journal of Chemical Information and Modeling

Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?

(2008) Andrew C. Good et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Community benchmarks for virtual screening

(2008) John J. Irwin   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints

(2008) Jennifer Venhorst et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel Agonists and Antagonists of the Free Fatty Acid Receptor 1 (FFAR1) Using Virtual Screening

(2008) Irina G. Tikhonova et al.   JOURNAL OF MEDICINAL CHEMISTRY

Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening

(2008) Yusuf Tanrikulu et al.   NATURE REVIEWS DRUG DISCOVERY

The use of ligand-based de novo design for scaffold hopping and sidechain optimization: Two case studies

(2007) Miklos Feher et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering

(2007) Daniel Muthas et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Prediction of protein–ligand complex structure by docking software guided by other complex structures

(2007) Yoshifumi Fukunishi et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING