Predicting protein–ligand affinity with a random matrix framework

Investigating Pharmacological Similarity by Charting Chemical Space

(2015) Rosa Buonfiglio et al.   Journal of Chemical Information and Modeling

Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives

(2015) Nathalie Lagarde et al.   Journal of Chemical Information and Modeling

An Aggregation Advisor for Ligand Discovery

(2015) John J. Irwin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular fingerprint similarity search in virtual screening

(2015) Adrià Cereto-Massagué et al.   METHODS

Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery

(2015) Woong-Hee Shin et al.   MOLECULES

Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

(2015) Dávid Bajusz et al.   Journal of Cheminformatics

Similarity-based modeling in large-scale prediction of drug-drug interactions

(2014) Santiago Vilar et al.   Nature Protocols

Molecular Similarity in Medicinal Chemistry

(2013) Gerald Maggiora et al.   JOURNAL OF MEDICINAL CHEMISTRY

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

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

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

DrugLogit: Logistic Discrimination between Drugs and Nondrugs Including Disease-Specificity by Assigning Probabilities Based on Molecular Properties

(2012) Alfonso T. García-Sosa et al.   Journal of Chemical Information and Modeling

Similarity Coefficients for Binary Chemoinformatics Data: Overview and Extended Comparison Using Simulated and Real Data Sets

(2012) Roberto Todeschini et al.   Journal of Chemical Information and Modeling

Classification of scaffold-hopping approaches

(2011) Hongmao Sun et al.   DRUG DISCOVERY TODAY

High-dimensional inference with the generalized Hopfield model: Principal component analysis and corrections

(2011) S. Cocco et al.   PHYSICAL REVIEW E

Computational chemogenomics

(2011) Edgar Jacoby   Wiley Interdisciplinary Reviews-Computational Molecular Science

Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach

(2010) Marc Bailly-Bechet et al.   BMC BIOINFORMATICS

Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

(2010) Madhavi Sastry et al.   Journal of Chemical Information and Modeling

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

Neuronal couplings between retinal ganglion cells inferred by efficient inverse statistical physics methods

(2009) S. Cocco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solubility Challenge: Can You Predict Solubilities of 32 Molecules Using a Database of 100 Reliable Measurements?

(2008) Antonio Llinàs et al.   Journal of Chemical Information and Modeling

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA