Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

(2016) A. Vangone et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Molecular Docking and Structure-Based Drug Design Strategies

(2015) Leonardo Ferreira et al.   MOLECULES

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology

(2015) Michael K. Gilson et al.   NUCLEIC ACIDS RESEARCH

Contacts-based prediction of binding affinity in protein–protein complexes

(2015) Anna Vangone et al.   eLife

Bile acid nuclear receptor FXR and digestive system diseases

(2015) Lili Ding et al.   Acta Pharmaceutica Sinica B

HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors

(2014) Panagiotis L. Kastritis et al.   Journal of Chemical Information and Modeling

fmcsR: mismatch tolerant maximum common substructure searching in R

(2013) Yan Wang et al.   BIOINFORMATICS

Advances in integrative modeling of biomolecular complexes

(2012) Ezgi Karaca et al.   METHODS

Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties

(2011) Hans G.F. Richter et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

Conformationally constrained farnesoid X receptor (FXR) agonists: Heteroaryl replacements of the naphthalene

(2010) Jonathan Y. Bass et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies

(2010) Justin A. Lemkul et al.   Journal of Chemical Information and Modeling

Plectasin, a Fungal Defensin, Targets the Bacterial Cell Wall Precursor Lipid II

(2010) T. Schneider et al.   SCIENCE

FXR agonist activity of conformationally constrained analogs of GW 4064

(2009) Adwoa Akwabi-Ameyaw et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Active-site architecture and catalytic mechanism of the lipid A deacylase LpxR ofSalmonella typhimurium

(2009) Lucy Rutten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Vancomycin−Nisin(1−12) Hybrid Restores Activity against Vancomycin Resistant Enterococci†

(2008) Christopher J. Arnusch et al.   BIOCHEMISTRY

ChemmineR: a compound mining framework for R

(2008) Y. Cao et al.   BIOINFORMATICS

Conformationally constrained farnesoid X receptor (FXR) agonists: Naphthoic acid-based analogs of GW 4064

(2008) Adwoa Akwabi-Ameyaw et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Principles of flexible protein-protein docking

(2008) Nelly Andrusier et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS