Network Measures for Chemical Library Design

Modeling genomic regulatory networks with big data

(2014) Hamid Bolouri   TRENDS IN GENETICS

Synthesis of Privileged Scaffolds by Using Diversity-Oriented Synthesis

(2013) Ramu Surakanti et al.   Chemistry-An Asian Journal

How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space

(2013) Alexios Koutsoukas et al.   Journal of Chemical Information and Modeling

In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naïve Bayes and Parzen-Rosenblatt Window

(2013) Alexios Koutsoukas et al.   Journal of Chemical Information and Modeling

Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds

(2013) Aaron M. Virshup et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

Exploring Activity Cliffs in Medicinal Chemistry

(2012) Dagmar Stumpfe et al.   JOURNAL OF MEDICINAL CHEMISTRY

Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action

(2011) Shan Zhao et al.   Annual Review of Pharmacology and Toxicology

The rise, fall and reinvention of combinatorial chemistry

(2011) Thomas Kodadek   CHEMICAL COMMUNICATIONS

Current Trends in Virtual High Throughput Screening Using Ligand-Based and Structure-Based Methods

(2011) Nagamani Sukumar et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Classification of scaffold-hopping approaches

(2011) Hongmao Sun et al.   DRUG DISCOVERY TODAY

Exploration of the Topology of Chemical Spaces with Network Measures

(2011) Michael P. Krein et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Diverging DOS Strategy Using an Allene-Containing Tryptophan Scaffold and a Library Design that Maximizes Biologically Relevant Chemical Space While Minimizing the Number of Compounds

(2011) Thomas O. Painter et al.   ACS Combinatorial Science

PESDserv: a server for high-throughput comparison of protein binding site surfaces

(2010) S. Das et al.   BIOINFORMATICS

Privileged scaffolds for library design and drug discovery

(2010) Matthew E Welsch et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe

(2010) Francesca Milletti et al.   Journal of Chemical Information and Modeling

Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures

(2010) Sourav Das et al.   Journal of Chemical Information and Modeling

Extended-Connectivity Fingerprints

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

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

PROMISCUOUS: a database for network-based drug-repositioning

(2010) J. von Eichborn et al.   NUCLEIC ACIDS RESEARCH

Diversity-oriented synthesis as a tool for the discovery of novel biologically active small molecules

(2010) Warren R.J.D. Galloway et al.   Nature Communications

The chemist as astronaut: Searching for biologically useful space in the chemical universe

(2009) David J. Triggle   BIOCHEMICAL PHARMACOLOGY

Navigating structure–activity landscapes

(2009) Jürgen Bajorath et al.   DRUG DISCOVERY TODAY

Small-World Phenomena in Chemical Library Networks: Application to Fragment-Based Drug Discovery

(2009) Naoki Tanaka et al.   Journal of Chemical Information and Modeling

Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions

(2009) Sourav Das et al.   Journal of Chemical Information and Modeling

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

QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets

(2009) Robert P. Sheridan et al.   Journal of Chemical Information and Modeling

An overview of the PubChem BioAssay resource

(2009) Yanli Wang et al.   NUCLEIC ACIDS RESEARCH

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

(2009) Sarah L. Kinnings et al.   PLoS Computational Biology

Burstiness and memory in complex systems

(2008) K.-I. Goh et al.   EPL

Assessing How Well a Modeling Protocol Captures a Structure−Activity Landscape

(2008) Rajarshi Guha et al.   Journal of Chemical Information and Modeling

Discovery of Power-Laws in Chemical Space

(2008) Ryan W. Benz et al.   Journal of Chemical Information and Modeling

Structure−Activity Landscape Index:  Identifying and Quantifying Activity Cliffs

(2008) Rajarshi Guha et al.   Journal of Chemical Information and Modeling

Structure−Activity Relationship Anatomy by Network-like Similarity Graphs and Local Structure−Activity Relationship Indices

(2008) Mathias Wawer et al.   JOURNAL OF MEDICINAL CHEMISTRY

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology