visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level

A mechanistic insight into protein-ligand interaction, folding, misfolding, aggregation and inhibition of protein aggregates: An overview

(2018) Tajalli Ilm Chandel et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization

(2017) Maria Kadukova et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An Intriguing Correlation Based on the Superimposition of Residue Pairs with Inhibitors that Target Protein-Protein Interfaces

(2016) Masakazu Nakadai et al.   Scientific Reports

LibME-automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein-ligand recognition

(2016) Wei He et al.   FEBS Open Bio

Hydrogen atoms can be located accurately and precisely by x-ray crystallography

(2016) M. Woinska et al.   Science Advances

Editorial: Alignment-free methods in computational biology

(2014) S. Vinga   BRIEFINGS IN BIOINFORMATICS

aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

APoc: large-scale identification of similar protein pockets

(2013) Mu Gao et al.   BIOINFORMATICS

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

(2013) O. Bonham-Carter et al.   BRIEFINGS IN BIOINFORMATICS

Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs

(2013) Jérémy Desaphy et al.   Journal of Chemical Information and Modeling

Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

(2013) Murat Can Cobanoglu et al.   Journal of Chemical Information and Modeling

Development of Highly Potent and Selective Diaminothiazole Inhibitors of Cyclin-Dependent Kinases

(2013) Ernst Schonbrunn et al.   JOURNAL OF MEDICINAL CHEMISTRY

Protein structure alignment beyond spatial proximity

(2013) Sheng Wang et al.   Scientific Reports

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins

(2013) Mu Gao et al.   PLoS Computational Biology

A survey of frequent subgraph mining algorithms

(2012) Chuntao Jiang et al.   KNOWLEDGE ENGINEERING REVIEW

HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids

(2011) V. M. Gonçalves-Almeida et al.   BIOINFORMATICS

Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns

(2011) Douglas EV Pires et al.   BMC GENOMICS

Pocketome: an encyclopedia of small-molecule binding sites in 4D

(2011) Irina Kufareva et al.   NUCLEIC ACIDS RESEARCH

Protein promiscuity and its implications for biotechnology

(2009) Irene Nobeli et al.   NATURE BIOTECHNOLOGY

Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins

(2008) Carlos H. da Silveira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS