Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding

Remote Thioredoxin Recognition Using Evolutionary Conservation and Structural Dynamics

(2011) Grace W. Tang et al.   STRUCTURE

Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites

(2010) Nathanaël Weill 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

In-Silico Approaches to Multi-target Drug Discovery

(2010) Xiao Hua Ma et al.   PHARMACEUTICAL RESEARCH

Basal Subtype and MAPK/ERK Kinase (MEK)-Phosphoinositide 3-Kinase Feedback Signaling Determine Susceptibility of Breast Cancer Cells to MEK Inhibition

(2009) O. K. Mirzoeva et al.   CANCER RESEARCH

QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets

(2009) Robert P. Sheridan et al.   Journal of Chemical Information and Modeling

ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI)

(2009) Wendy A. Warr   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Selectively Nonselective Kinase Inhibition: Striking the Right Balance

(2009) Richard Morphy   JOURNAL OF MEDICINAL CHEMISTRY

Prediction of calcium-binding sites by combining loop-modeling with machine learning

(2009) Tianyun Liu et al.   BMC STRUCTURAL BIOLOGY

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

(2009) Li Xie et al.   PLoS Computational Biology

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites

(2008) R. Najmanovich et al.   BIOINFORMATICS

How to Measure the Similarity Between Protein Ligand-Binding Sites?

(2008) Esther Kellenberger et al.   Current Computer-Aided Drug Design

Quantifying the Relationships among Drug Classes

(2008) Jérôme Hert et al.   Journal of Chemical Information and Modeling

A quantitative analysis of kinase inhibitor selectivity

(2008) Mazen W Karaman et al.   NATURE BIOTECHNOLOGY

Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases

(2008) Beth Apsel et al.   Nature Chemical Biology

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A simple and fuzzy method to align and compare druggable ligand-binding sites

(2008) Claire Schalon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation

(2008) Shirley Wu et al.   GENOME BIOLOGY

Inhibition of casein kinase 1-epsilon induces cancer-cell-selective, PERIOD2-dependent growth arrest

(2008) Wan Seok Yang et al.   GENOME BIOLOGY

MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison

(2002) Angel R. Ortiz et al.   PROTEIN SCIENCE