PDB-Explorer: a web-based interactive map of the protein data bank in shape space

The Chemical Space Project

(2015) Jean-Louis Reymond   ACCOUNTS OF CHEMICAL RESEARCH

Similarity Mapplet: Interactive Visualization of the Directory of Useful Decoys and ChEMBL in High Dimensional Chemical Spaces

(2015) Mahendra Awale et al.   Journal of Chemical Information and Modeling

Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia

(2015) Peter Ertl et al.   Journal of Cheminformatics

Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17

(2014) Mahendra Awale et al.   Journal of Chemical Information and Modeling

The role of ligand efficiency metrics in drug discovery

(2014) Andrew L. Hopkins et al.   NATURE REVIEWS DRUG DISCOVERY

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

A series of PDB-related databanks for everyday needs

(2014) Wouter G. Touw et al.   NUCLEIC ACIDS RESEARCH

Cyclodextrin-based multivalent glycodisplays: covalent and supramolecular conjugates to assess carbohydrate–protein interactions

(2013) Álvaro Martínez et al.   CHEMICAL SOCIETY REVIEWS

MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13

(2013) Mahendra Awale et al.   Journal of Chemical Information and Modeling

SMIfp (SMILES fingerprint) Chemical Space for Virtual Screening and Visualization of Large Databases of Organic Molecules

(2013) Julian Schwartz et al.   Journal of Chemical Information and Modeling

Protein pocket and ligand shape comparison and its application in virtual screening

(2013) Matthias Wirth et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

SCOP2 prototype: a new approach to protein structure mining

(2013) Antonina Andreeva et al.   NUCLEIC ACIDS RESEARCH

MMDB and VAST+: tracking structural similarities between macromolecular complexes

(2013) Thomas Madej et al.   NUCLEIC ACIDS RESEARCH

PDBe: Protein Data Bank in Europe

(2013) Aleksandras Gutmanas et al.   NUCLEIC ACIDS RESEARCH

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

The RCSB Protein Data Bank: new resources for research and education

(2012) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Pre-calculated protein structure alignments at the RCSB PDB website: Fig. 1.

(2010) Andreas Prlić et al.   BIOINFORMATICS

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

3D-SURFER: software for high-throughput protein surface comparison and analysis

(2009) David La et al.   BIOINFORMATICS

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

Autoproteolytic Activity Derived from the Infectious Bursal Disease Virus Capsid Protein

(2009) Nerea Irigoyen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal Structure of an Aquabirnavirus Particle: Insights into Antigenic Diversity and Virulence Determinism

(2009) F. Coulibaly et al.   JOURNAL OF VIROLOGY

Investigation of Atomic Level Patterns in Protein—Small Ligand Interactions

(2009) Ke Chen et al.   PLoS One

Comparison of structure-based and threading-based approaches to protein functional annotation

(2009) Michal Brylinski et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

(2009) Alison Cuff et al.   STRUCTURE

Matt: Local Flexibility Aids Protein Multiple Structure Alignment

(2008) Matthew Menke et al.   PLoS Computational Biology

Fast protein tertiary structure retrieval based on global surface shape similarity

(2008) Lee Sael et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS