A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

(2017) Ross McGuire et al.   Journal of Chemical Information and Modeling

Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects

(2017) Matthieu Chartier et al.   BMC Pharmacology & Toxicology

Protein Binding Pocket Dynamics

(2016) Antonia Stank et al.   ACCOUNTS OF CHEMICAL RESEARCH

Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case

(2016) Lydia Siragusa et al.   ChemMedChem

CavSimBase: A Database for Large Scale Comparison of Protein Binding Sites

(2016) Matthias Leinweber et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Identification and Visualization of Kinase-Specific Subpockets

(2016) Andrea Volkamer et al.   Journal of Chemical Information and Modeling

SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles

(2016) Stefan Bietz et al.   Journal of Chemical Information and Modeling

Prediction of Protein Pairs Sharing Common Active Ligands Using Protein Sequence, Structure, and Ligand Similarity

(2016) Yu-Chen Chen et al.   Journal of Chemical Information and Modeling

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015

(2016) Inna Slynko et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design

(2016) Christiane Ehrt et al.   JOURNAL OF MEDICINAL CHEMISTRY

Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach

(2016) Zheng Zhao et al.   JOURNAL OF MEDICINAL CHEMISTRY

Modeling Tanimoto Similarity Value Distributions and Predicting Search Results

(2016) Martin Vogt et al.   Molecular Informatics

The ChEMBL database in 2017

(2016) Anna Gaulton et al.   NUCLEIC ACIDS RESEARCH

Mapping the 3D structures of small molecule binding sites

(2016) Joshua Meyers et al.   Journal of Cheminformatics

Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance

(2016) Ludovic Chaput et al.   Journal of Cheminformatics

The Recognition of Identical Ligands by Unrelated Proteins

(2015) Sarah Barelier et al.   ACS Chemical Biology

Statin-Induced Myopathy Is Associated with Mitochondrial Complex III Inhibition

(2015) Tom J.J. Schirris et al.   Cell Metabolism

Detection of Binding Site Molecular Interaction Field Similarities

(2015) Matthieu Chartier et al.   Journal of Chemical Information and Modeling

Structure-Based Prediction of G-Protein-Coupled Receptor Ligand Function: A β-Adrenoceptor Case Study

(2015) Albert J. Kooistra et al.   Journal of Chemical Information and Modeling

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design

(2015) Shane Ó Conchúir et al.   PLoS One

Computational discovery and experimental verification of tyrosine kinase inhibitor pazopanib for the reversal of memory and cognitive deficits in rat model neurodegeneration

(2015) Yongliang Yang et al.   Chemical Science

Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization

(2015) Tamer M Ibrahim et al.   Journal of Cheminformatics

Mitochondrial ADP/ATP exchange inhibition: a novel off-target mechanism underlying ibipinabant-induced myotoxicity

(2015) Tom J. J. Schirris et al.   Scientific Reports

Similarities between the Binding Sites of SB-206553 at Serotonin Type 2 and Alpha7 Acetylcholine Nicotinic Receptors: Rationale for Its Polypharmacological Profile

(2015) Patricia Möller-Acuña et al.   PLoS One

A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

(2014) Mathieu Larocque et al.   BMC Systems Biology

Exploiting structural information for drug-target assessment

(2014) Andrea Volkamer et al.   Future Medicinal Chemistry

Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real

(2014) Timo Krotzky et al.   Journal of Chemical Information and Modeling

PLIC: protein–ligand interaction clusters

(2014) Praveen Anand et al.   Database-The Journal of Biological Databases and Curation

SiteHopper - a unique tool for binding site comparison

(2014) Jose Batista et al.   Journal of Cheminformatics

Exploring the role of receptor flexibility in structure-based drug discovery

(2013) Ferran Feixas et al.   BIOPHYSICAL CHEMISTRY

Structural Bioinformatics-Based Identification of EGFR Inhibitor Gefitinib as a Putative Lead Compound for BACE

(2013) Mingshan Niu et al.   Chemical Biology & Drug Design

Binding site comparison for function prediction and pharmaceutical discovery

(2013) Janez Konc et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding

(2013) Tal Keren-Kaplan et al.   EMBO JOURNAL

Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs

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

Identification of Similar Binding Sites to Detect Distant Polypharmacology

(2013) Xavier Jalencas et al.   Molecular Informatics

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key

(2013) V. Joachim Haupt et al.   PLoS One

Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

(2013) Janez Konc et al.   PLoS Computational Biology

Rethinking Molecular Similarity: Comparing Compounds on the Basis of Biological Activity

(2012) Paula M. Petrone et al.   ACS Chemical Biology

Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement

(2012) David J. Wood et al.   Journal of Chemical Information and Modeling

ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures

(2012) Janez Konc et al.   Journal of Chemical Information and Modeling

Structural Insights into the Molecular Basis of the Ligand Promiscuity

(2012) Noé Sturm et al.   Journal of Chemical Information and Modeling

GRID-Based Three-Dimensional Pharmacophores II: PharmBench, a Benchmark Data Set for Evaluating Pharmacophore Elucidation Methods

(2012) Simon Cross et al.   Journal of Chemical Information and Modeling

Comparison and Druggability Prediction of Protein–Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes

(2012) Jérémy Desaphy et al.   Journal of Chemical Information and Modeling

SwissSidechain: a molecular and structural database of non-natural sidechains

(2012) David Gfeller et al.   NUCLEIC ACIDS RESEARCH

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

Druggability predictions: methods, limitations, and applications

(2012) Xavier Barril   Wiley Interdisciplinary Reviews-Computational Molecular Science

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Old friends in new guise: repositioning of known drugs with structural bioinformatics

(2011) V. J. Haupt et al.   BRIEFINGS IN BIOINFORMATICS

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery

(2011) Roman A. Laskowski et al.   Journal of Chemical Information and Modeling

Combining Global and Local Measures for Structure-Based Druggability Predictions

(2011) Andrea Volkamer et al.   Journal of Chemical Information and Modeling

PoSSuM: a database of similar protein-ligand binding and putative pockets

(2011) J.-I. Ito et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Irina Kufareva et al.   NUCLEIC ACIDS RESEARCH

Structural Annotation of Mycobacterium tuberculosis Proteome

(2011) Praveen Anand et al.   PLoS One

Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir

(2011) Li Xie et al.   PLoS Computational Biology

Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding

(2011) Tianyun Liu et al.   PLoS Computational Biology

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

(2010) Janez Konc et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation

(2010) Gong-Hua Li et al.   BMC BIOINFORMATICS

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

(2010) Brice Hoffmann et al.   BMC BIOINFORMATICS

Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites

(2010) Nathanaël Weill et al.   Journal of Chemical Information and Modeling

When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values

(2010) Pierre Baldi et al.   Journal of Chemical Information and Modeling

Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

(2010) Peter Schmidtke et al.   JOURNAL OF MEDICINAL CHEMISTRY

Scaffold Hopping Using Two-Dimensional Fingerprints: True Potential, Black Magic, or a Hopeless Endeavor? Guidelines for Virtual Screening

(2010) Martin Vogt et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identifying Unexpected Therapeutic Targets via Chemical-Protein Interactome

(2010) Lun Yang et al.   PLoS One

Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements

(2010) Enrico De Franchi et al.   PLoS One

A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

(2009) L. Xie et al.   BIOINFORMATICS

PocketMatch: A new algorithm to compare binding sites in protein structures

(2009) Kalidas Yeturu et al.   BMC BIOINFORMATICS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family

(2009) Sarah L. Kinnings et al.   Journal of Chemical Information and Modeling

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins

(2009) Abdullah Kahraman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How to Measure the Similarity Between Protein Ligand-Binding Sites?

(2008) Esther Kellenberger et al.   Current Computer-Aided Drug Design

Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles

(2008) Sidhartha Chaudhury et al.   JOURNAL OF MOLECULAR BIOLOGY

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A simple and fuzzy method to align and compare druggable ligand-binding sites

(2008) Claire Schalon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS