Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge

Neuritogenic Militarinone-Inspired 4-Hydroxypyridones Target the Stress Pathway Kinase MAP4K4

(2015) Peter Schröder et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

(2015) Richard D. Smith et al.   Journal of Chemical Information and Modeling

Structure-Based Design of GNE-495, a Potent and Selective MAP4K4 Inhibitor with Efficacy in Retinal Angiogenesis

(2015) Chudi O. Ndubaku et al.   ACS Medicinal Chemistry Letters

Fragment-based identification and optimization of a class of potent pyrrolo[2,1- f ][1,2,4]triazine MAP4K4 inhibitors

(2014) Lan Wang et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

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

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure

(2012) D. R. Koes et al.   NUCLEIC ACIDS RESEARCH

ZINCPharmer: pharmacophore search of the ZINC database

(2012) D. R. Koes et al.   NUCLEIC ACIDS RESEARCH

Enabling Large-Scale Design, Synthesis and Validation of Small Molecule Protein-Protein Antagonists

(2012) David Koes et al.   PLoS One

Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein–Ligand Binding Geometry and Free Energy

(2011) Obaidur Rahaman et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

(2011) James B. Dunbar et al.   Journal of Chemical Information and Modeling

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

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

Open3DALIGN: an open-source software aimed at unsupervised ligand alignment

(2011) Paolo Tosco et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields

(2010) Paolo Tosco et al.   JOURNAL OF MOLECULAR MODELING

Protein Kinase−Inhibitor Database: Structural Variability of and Inhibitor Interactions with the Protein Kinase P-Loop

(2010) Ronak Y. Patel et al.   JOURNAL OF PROTEOME RESEARCH

Inside the Hsp90 inhibitors binding mode through induced fit docking

(2008) Antonino Lauria et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING