Focused grid-based resampling for protein docking and mapping

The Impact of Side-Chain Packing on Protein Docking Refinement

(2015) Mohammad Moghadasi et al.   Journal of Chemical Information and Modeling

Energy Minimization on Manifolds for Docking Flexible Molecules

(2015) Hanieh Mirzaei et al.   Journal of Chemical Theory and Computation

New Frontiers in Druggability

(2015) Dima Kozakov et al.   JOURNAL OF MEDICINAL CHEMISTRY

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

(2015) Dima Kozakov et al.   Nature Protocols

Ligand deconstruction: Why some fragment binding positions are conserved and others are not

(2015) Dima Kozakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fragment-Based Lead Discovery and Design

(2014) Diane Joseph-McCarthy et al.   Journal of Chemical Information and Modeling

Structure-Guided Design and Optimization of Small Molecules Targeting the Protein–Protein Interaction between the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities

(2014) Carles Galdeano et al.   JOURNAL OF MEDICINAL CHEMISTRY

Small molecules inhibit the interaction of Nrf2 and the Keap1 Kelch domain through a non-covalent mechanism

(2013) Douglas Marcotte et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Sampling and scoring: A marriage made in heaven

(2013) Sandor Vajda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How good is automated protein docking?

(2013) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein–Protein Interactions?

(2013) David M. Dias et al.   ACS Medicinal Chemistry Letters

Dissecting Fragment-Based Lead Discovery at the von Hippel-Lindau Protein:Hypoxia Inducible Factor 1α Protein-Protein Interface

(2012) Inge Van Molle et al.   CHEMISTRY & BIOLOGY

Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1α Interaction

(2012) Dennis L. Buckley et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural Basis for Recognition of H3T3ph and Smac/DIABLO N-terminal Peptides by Human Survivin

(2012) Jiamu Du et al.   STRUCTURE

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

(2011) Chi-Ho Ngan et al.   BIOINFORMATICS

Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery

(2011) David R. Hall et al.   Journal of Chemical Information and Modeling

Analysis of Binding Site Hot Spots on the Surface of Ras GTPase

(2011) Greg Buhrman et al.   JOURNAL OF MOLECULAR BIOLOGY

Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme

(2011) David H. Hall et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural conservation of druggable hot spots in protein-protein interfaces

(2011) D. Kozakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent Advances in Anti-Survivin Treatments for Cancer

(2010) R. Kanwar et al.   CURRENT MEDICINAL CHEMISTRY

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Where does amantadine bind to the influenza virus M2 proton channel?

(2010) Dima Kozakov et al.   TRENDS IN BIOCHEMICAL SCIENCES

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

(2009) Ryan Brenke et al.   BIOINFORMATICS

Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel

(2009) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

(2009) Melissa R. Landon et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

Discrimination of near-native structures in protein-protein docking by testing the stability of local minima

(2008) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 3.0

(2008) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

(2008) Yang Shen et al.   PLoS Computational Biology