Recent trends and observations in the design of high-quality screening collections

A Scaffold-Tree-Merging Strategy for Prospective Bioactivity Annotation of γ-Pyrones

(2010) Stefan Wetzel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Drug Discovery with DNA-Encoded Chemical Libraries

(2010) Fabian Buller et al.   BIOCONJUGATE CHEMISTRY

Architectural Repertoire of Ligand-Binding Pockets on Protein Surfaces

(2010) Martin Weisel et al.   CHEMBIOCHEM

Chemical Space Sampling in Virtual Screening by Different Crystal Structures

(2010) Natasja Brooijmans et al.   Chemical Biology & Drug Design

Structural and Potency Relationships between Scaffolds of Compounds Active against Human Targets

(2010) Ye Hu et al.   ChemMedChem

Selecting chemicals: the emerging utility of DNA-encoded libraries

(2010) Matthew A. Clark   CURRENT OPINION IN CHEMICAL BIOLOGY

Enhancements of screening collections to address areas of unmet medical need: an industry perspective

(2010) David H Drewry et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Privileged scaffolds for library design and drug discovery

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

Apparent activity in high-throughput screening: origins of compound-dependent assay interference

(2010) Natasha Thorne et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Structural biology in fragment-based drug design

(2010) Christopher W Murray et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Editorial [Hot topic: Macrocycles in Medicinal Chemistry and Drug Discovery (Guest Editors: Adegboyega K. Oyelere)]

(2010) Adegboyega K. Oyelere   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation

(2010) Cele Abad-Zapatero et al.   DRUG DISCOVERY TODAY

Lipophilicity in drug discovery

(2010) Michael J Waring   Expert Opinion on Drug Discovery

Observations on screening-based research and some concerning trends in the literature

(2010) Jonathan B Baell   Future Medicinal Chemistry

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

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

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

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

Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase−Ligand Interactions

(2010) Mengzhu Xue et al.   Journal of Chemical Information and Modeling

Compound Set Enrichment: A Novel Approach to Analysis of Primary HTS Data

(2010) Thibault Varin et al.   Journal of Chemical Information and Modeling

Pasireotide (SOM230) Demonstrates Efficacy and Safety in Patients with Acromegaly: A Randomized, Multicenter, Phase II Trial

(2010) S. Petersenn et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Chemical space sampling by different scoring functions and crystal structures

(2010) Natasja Brooijmans et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Investigation of the Relationship between Topology and Selectivity for Druglike Molecules

(2010) Yidong Yang 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

New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays

(2010) Jonathan B. Baell et al.   JOURNAL OF MEDICINAL CHEMISTRY

Bioisosteric Replacement and Scaffold Hopping in Lead Generation and Optimization

(2010) Sarah R. Langdon et al.   Molecular Informatics

Preparation, characterization andin silicomodeling of biodegradable nanoparticles containing cyclosporine A and coenzyme Q10

(2010) D D Ankola et al.   NANOTECHNOLOGY

Small-molecule inhibition of APT1 affects Ras localization and signaling

(2010) Frank J Dekker et al.   Nature Chemical Biology

Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery

(2010) Wolfgang Jahnke et al.   Nature Chemical Biology

Highly enantioselective synthesis and cellular evaluation of spirooxindoles inspired by natural products

(2010) Andrey P. Antonchick et al.   Nature Chemistry

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

Chemical space as a source for new drugs

(2010) Jean-Louis Reymond et al.   MedChemComm

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

Principles, implementation, and application of biology-oriented synthesis (BIOS)

(2009) Wolfram Wilk et al.   BIOLOGICAL CHEMISTRY

The protein meta-structure: a novel concept for chemical and molecular biology

(2009) Robert Konrat   CELLULAR AND MOLECULAR LIFE SCIENCES

Utilizing Target-Ligand Interaction Information in Fingerprint Searching for Ligands of Related Targets

(2009) Lu Tan et al.   Chemical Biology & Drug Design

The discovery of antibacterial agents using diversity-oriented synthesis

(2009) Warren R. J. D. Galloway et al.   CHEMICAL COMMUNICATIONS

SHOP: A Method For Structure-Based Fragment and Scaffold Hopping

(2009) Fabien Fontaine et al.   ChemMedChem

Scaffold Distributions in Bioactive Molecules, Clinical Trials Compounds, and Drugs

(2009) Ye Hu et al.   ChemMedChem

Chemogenomic Strategies to Expand the Bioactive Chemical Space

(2009) E. Jacoby et al.   CURRENT MEDICINAL CHEMISTRY

Recent progress in fragment-based lead discovery

(2009) Michèle N Schulz et al.   CURRENT OPINION IN PHARMACOLOGY

Designing Multiple Ligands – Medicinal Chemistry Strategies and Challenges

(2009) Richard Morphy et al.   CURRENT PHARMACEUTICAL DESIGN

The impact of aromatic ring count on compound developability – are too many aromatic rings a liability in drug design?

(2009) Timothy J. Ritchie et al.   DRUG DISCOVERY TODAY

Targeted scoring functions for virtual screening

(2009) Markus H.J. Seifert   DRUG DISCOVERY TODAY

From fragment to clinical candidate—a historical perspective

(2009) Gianni Chessari et al.   DRUG DISCOVERY TODAY

Epigenetic opportunities and challenges in cancer

(2009) Jonathan D. Best et al.   DRUG DISCOVERY TODAY

Solid Lipid Nanoparticles as Insulin Inhalation Carriers for Enhanced Pulmonary Delivery

(2009) Ru Bi et al.   Journal of Biomedical Nanotechnology

Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner

(2009) Eelke van der Horst et al.   Journal of Chemical Information and Modeling

Predicting Multiple Ligand Binding Modes Using Self-Consistent Pharmacophore Hypotheses

(2009) Izhar Wallach et al.   Journal of Chemical Information and Modeling

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening

(2009) Violeta I. Pérez-Nueno et al.   Journal of Chemical Information and Modeling

Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis

(2009) Josef Scheiber 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

Robust optimization of scoring functions for a target class

(2009) Markus H. J. Seifert   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Lessons for fragment library design: analysis of output from multiple screening campaigns

(2009) I-Jen Chen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Identification of Lead Compounds As Antagonists of Protein Bcl-xLwith a Diversity-Oriented Multidisciplinary Approach

(2009) Simone Di Micco et al.   JOURNAL OF MEDICINAL CHEMISTRY

Heteroaromatic Rings of the Future

(2009) William R. Pitt et al.   JOURNAL OF MEDICINAL CHEMISTRY

Mapping Adverse Drug Reactions in Chemical Space

(2009) Josef Scheiber et al.   JOURNAL OF MEDICINAL CHEMISTRY

Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success

(2009) Frank Lovering et al.   JOURNAL OF MEDICINAL CHEMISTRY

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13

(2009) Lorenz C. Blum et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ribosomally Synthesized Thiopeptide Antibiotics Targeting Elongation Factor Tu

(2009) Rowan P. Morris et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Bioactivity-guided mapping and navigation of chemical space

(2009) Steffen Renner et al.   Nature Chemical Biology

Interactive exploration of chemical space with Scaffold Hunter

(2009) Stefan Wetzel et al.   Nature Chemical Biology

Quantifying biogenic bias in screening libraries

(2009) Jérôme Hert et al.   Nature Chemical Biology

Open access chemical and clinical probes to support drug discovery

(2009) Aled M Edwards et al.   Nature Chemical Biology

Combining docking with pharmacophore filtering for improved virtual screening

(2009) Megan L Peach et al.   Journal of Cheminformatics

Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening

(2009) Nobuyoshi Nagamine et al.   PLoS Computational Biology

Anti-MRSA Agent Discovery Using Diversity-Oriented Synthesis

(2008) Gemma L. Thomas et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Chemical substructures that enrich for biological activity

(2008) Justin Klekota et al.   BIOINFORMATICS

NVP-AUY922: A Novel Heat Shock Protein 90 Inhibitor Active against Xenograft Tumor Growth, Angiogenesis, and Metastasis

(2008) S. A. Eccles et al.   CANCER RESEARCH

How Large Does a Compound Screening Collection Need To Be?

(2008) Michael Lipkin et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

A Ligand-Based Approach to Mining the Chemogenomic Space of Drugs

(2008) Elisabet Gregori-Puigjane et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Recent Progress in the Discovery of Macrocyclic Compounds as Potential Anti-Infective Therapeutics

(2008) D. Obrecht et al.   CURRENT MEDICINAL CHEMISTRY

‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries

(2008) Paul D. Dobson et al.   DRUG DISCOVERY TODAY

Maximum Common Binding Modes (MCBM):  Consensus Docking Scoring Using Multiple Ligand Information and Interaction Fingerprints

(2008) Steffen Renner et al.   Journal of Chemical Information and Modeling

Homology Model-Based Virtual Screening for GPCR Ligands Using Docking and Target-Biased Scoring

(2008) Tanja Weil et al.   Journal of Chemical Information and Modeling

Scaffold Hopping in Drug Discovery Using Inductive Logic Programming

(2008) Kazuhisa Tsunoyama et al.   Journal of Chemical Information and Modeling

Surrogate AutoShim: Predocking into a Universal Ensemble Kinase Receptor for Three Dimensional Activity Prediction, Very Quickly, without a Crystal Structure

(2008) Eric J. Martin et al.   Journal of Chemical Information and Modeling

AutoShim: Empirically Corrected Scoring Functions for Quantitative Docking with a Crystal Structure and IC50Training Data

(2008) Eric J. Martin et al.   Journal of Chemical Information and Modeling

Ranking Targets in Structure-Based Virtual Screening of Three-Dimensional Protein Libraries: Methods and Problems

(2008) Esther Kellenberger et al.   Journal of Chemical Information and Modeling

Treatment of Pituitary-Dependent Cushing’s Disease with the Multireceptor Ligand Somatostatin Analog Pasireotide (SOM230): A Multicenter, Phase II Trial

(2008) M. Boscaro et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Kinase-likeness and Kinase-Privileged Fragments: Toward Virtual Polypharmacology

(2008) Alex M. Aronov et al.   JOURNAL OF MEDICINAL CHEMISTRY

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

(2008) Giovanni Bottegoni et al.   JOURNAL OF MEDICINAL CHEMISTRY

3-D clustering: a tool for high throughput docking

(2008) John P. Priestle   JOURNAL OF MOLECULAR MODELING

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The exploration of macrocycles for drug discovery — an underexploited structural class

(2008) Edward M. Driggers et al.   NATURE REVIEWS DRUG DISCOVERY

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE

Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries

(2007) Peter Ertl et al.   Journal of Chemical Information and Modeling