Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Virtual Fragment Docking by Glide: a Validation Study on 190 Protein−Fragment Complexes

(2010) Márk Sándor et al.   Journal of Chemical Information and Modeling

Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

(2010) Ian R. Craig et al.   Journal of Chemical Information and Modeling

LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops

(2010) Paul Labute   Journal of Chemical Information and Modeling

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma

(2010) Gideon Bollag et al.   NATURE

Docking and chemoinformatic screens for new ligands and targets

(2009) Peter Kolb et al.   CURRENT OPINION IN BIOTECHNOLOGY

Transforming fragments into candidates: small becomes big in medicinal chemistry

(2009) Gerdien E. de Kloe et al.   DRUG DISCOVERY TODAY

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide

(2009) Sameer Kawatkar et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular docking and ligand specificity in fragment-based inhibitor discovery

(2009) Yu Chen et al.   Nature Chemical Biology

The rise of fragment-based drug discovery

(2009) Christopher W. Murray et al.   Nature Chemistry

Docking for fragment inhibitors of AmpC  -lactamase

(2009) D. G. Teotico et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Blind docking of pharmaceutically relevant compounds using RosettaLigand

(2009) Ian W. Davis et al.   PROTEIN SCIENCE

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improving database enrichment through ensemble docking

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

Fragment-Based Design of Small Molecule X-Linked Inhibitor of Apoptosis Protein Inhibitors

(2008) Jui-Wen Huang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Recent Developments in Fragment-Based Drug Discovery

(2008) Miles Congreve et al.   JOURNAL OF MEDICINAL CHEMISTRY

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

(2008) Andreas May et al.   JOURNAL OF MEDICINAL CHEMISTRY

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis et al.   JOURNAL OF MOLECULAR BIOLOGY

Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent

(2008) D. R. Artis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity

(2008) J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking

(2008) Erin S. D. Bolstad et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS