Protein–ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein–Ligand Interfaces

(2017) Eva Nittinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

CATH: an expanded resource to predict protein function through structure and sequence

(2016) Natalie L. Dawson et al.   NUCLEIC ACIDS RESEARCH

Detecting the native ligand orientation by interfacial rigidity: SiteInterlock

(2016) Sebastian Raschka et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

(2015) Michael Feig et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Interaction between bound water molecules and local protein structures: A statistical analysis of the hydrogen bond structures around bound water molecules

(2015) Seungpyo Hong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

(2014) Aqeel Ahmed et al.   NUCLEIC ACIDS RESEARCH

Essential considerations for using protein–ligand structures in drug discovery

(2012) Gregory L. Warren et al.   DRUG DISCOVERY TODAY

A synthetic hexapeptide designed to resemble a proteinaceous p-loop nest is shown to bind inorganic phosphate

(2012) Antonio Bianchi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes

(2011) Gerd Neudert et al.   Journal of Chemical Information and Modeling

Scoring ligand similarity in structure-based virtual screening

(2009) Maria I. Zavodszky et al.   JOURNAL OF MOLECULAR RECOGNITION

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8

(2009) Elmar Krieger et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS