De novodesign: balancing novelty and confined chemical space

Piperazine sulfonamide BACE1 inhibitors: Design, synthesis, and in vivo characterization

(2010) Jared Cumming et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Understanding Kinase Selectivity Through Energetic Analysis of Binding Site Waters

(2010) Daniel D. Robinson et al.   ChemMedChem

Computational Approaches for Fragment-Based and De Novo Design

(2010) Kathryn Loving et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

De Novo Design of a Picomolar Nonbasic 5-HT1BReceptor Antagonist

(2010) David A. Nugiel et al.   JOURNAL OF MEDICINAL CHEMISTRY

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Structure-based design of substituted biphenyl ethylene ethers as ligands binding in the hydrophobic pocket of gp41 and blocking the helical bundle formation

(2009) Bin Liu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Structure-based de novo design and biochemical evaluation of novel Cdc25 phosphatase inhibitors

(2009) Hwangseo Park et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Design and synthesis of new hydroxyethylamines as inhibitors of d-alanyl-d-lactate ligase (VanA) and d-alanyl-d-alanine ligase (DdlB)

(2009) Matej Sova et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Discovery of a novel HCV helicase inhibitor by a de novo drug design approach

(2009) Sahar Kandil et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Structure-based design, synthesis and biological evaluation of new N-carboxyphenylpyrrole derivatives as HIV fusion inhibitors targeting gp41

(2009) Yong Wang et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

AutoGrow: A Novel Algorithm for Protein Inhibitor Design

(2009) Jacob D. Durrant et al.   Chemical Biology & Drug Design

Scaffold-Hopping Potential of Fragment-Based De Novo Design: The Chances and Limits of Variation

(2009) Bjoern Krueger et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Docking, virtual high throughput screening and in silico fragment-based drug design

(2009) Vincent Zoete et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

E-Novo: An Automated Workflow for Efficient Structure-Based Lead Optimization

(2009) Bradley C. Pearce et al.   Journal of Chemical Information and Modeling

FOG: Fragment Optimized Growth Algorithm for thede NovoGeneration of Molecules Occupying Druglike Chemical Space

(2009) Peter S. Kutchukian et al.   Journal of Chemical Information and Modeling

Fragment Shuffling: An Automated Workflow for Three-Dimensional Fragment-Based Ligand Design

(2009) Britta Nisius et al.   Journal of Chemical Information and Modeling

De Novo Drug Design Using Multiobjective Evolutionary Graphs

(2009) Christos A. Nicolaou et al.   Journal of Chemical Information and Modeling

Knowledge-Based Approach tode NovoDesign Using Reaction Vectors

(2009) Hina Patel et al.   Journal of Chemical Information and Modeling

Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation

(2009) James Law et al.   Journal of Chemical Information and Modeling

LoFT: Similarity-Driven Multiobjective Focused Library Design

(2009) J. Robert Fischer et al.   Journal of Chemical Information and Modeling

Second-generation de novo design: a view from a medicinal chemist perspective

(2009) Andrea Zaliani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Kinase Inhibitor Data Modeling and de Novo Inhibitor Design with Fragment Approaches

(2009) Michal Vieth et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Highly Potent and Selective Inhibitors of Neuronal Nitric Oxide Synthase by Fragment Hopping

(2009) Haitao Ji et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovering Potent Small Molecule Inhibitors of Cyclophilin A Using de Novo Drug Design Approach

(2009) Shuaishuai Ni et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure-Based Design, Synthesis, and Characterization of Inhibitors of Human andPlasmodium falciparumDihydroorotate Dehydrogenases†

(2009) Matthew Davies et al.   JOURNAL OF MEDICINAL CHEMISTRY

Prediction of the Water Content in Protein Binding Sites

(2009) Julien Michel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

In Silico Improvement of β3-Peptide Inhibitors of p53•hDM2 and p53•hDMX

(2009) Julien Michel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

(2009) Julien Michel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Interactive exploration of chemical space with Scaffold Hunter

(2009) Stefan Wetzel et al.   Nature Chemical Biology

Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor

(2009) K. Biggadike et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-energy water sites determine peptide binding affinity and specificity of PDZ domains

(2009) Thijs Beuming et al.   PROTEIN SCIENCE

Structure-Based Design of Benzoxazoles as new Inhibitors for D-Alanyl – D-Alanine Ligase

(2009) Isabelle Tytgat et al.   Quantitative structure-activity relationships & combinatorial science

Structure-based design and subsequent optimization of 2-tolyl-(1,2,3-triazol-1-yl-4-carboxamide) inhibitors of p38 MAP kinase

(2008) D.A. Cogan et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors

(2008) J.N. Cumming et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Molecular modeling, synthesis, and activity studies of novel biaryl and fused-ring BACE1 inhibitors

(2008) Srinivas Reddy Chirapu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Ligand-Based Approaches in Virtual Screening

(2008) Dominique Douguet   Current Computer-Aided Drug Design

In Silico Prediction of Drug Properties

(2008) M. Hutter   CURRENT MEDICINAL CHEMISTRY

Self-Organizing Maps in Drug Discovery: Compound Library Design, Scaffold-Hopping, Repurposing

(2008) P. Schneider et al.   CURRENT MEDICINAL CHEMISTRY

Gradual in Silico Filtering for Druglike Substances

(2008) Nadine Schneider et al.   Journal of Chemical Information and Modeling

De Novo Ligand Design to Partially Flexible Active Sites:  Application of the ReFlex Algorithm to Carboxypeptidase A, Acetylcholinesterase, and the Estrogen Receptor

(2008) Stuart Firth-Clark et al.   Journal of Chemical Information and Modeling

Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization

(2008) Fabian Dey et al.   Journal of Chemical Information and Modeling

Benzodioxoles: Novel Cannabinoid-1 Receptor Inverse Agonists for the Treatment of Obesity

(2008) Leo Alig et al.   JOURNAL OF MEDICINAL CHEMISTRY

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

(2008) Alessio Amadasi et al.   JOURNAL OF MEDICINAL CHEMISTRY

Minimal Pharmacophoric Elements and Fragment Hopping, an Approach Directed at Molecular Diversity and Isozyme Selectivity. Design of Selective Neuronal Nitric Oxide Synthase Inhibitors

(2008) Haitao Ji et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Design, synthesis, antifungal activity, and ADME prediction of functional analogues of terbinafine

(2008) Prashant S. Kharkar et al.   MEDICINAL CHEMISTRY RESEARCH

Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase

(2008) Anil K. Agarwal et al.   TETRAHEDRON

Voyages to the (un)known: adaptive design of bioactive compounds

(2008) Gisbert Schneider et al.   TRENDS IN BIOTECHNOLOGY

Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers

(2008) Jihua Hao et al.   PLoS Computational Biology

Design and SAR of selective T-type calcium channel antagonists containing a biaryl sulfonamide core

(2007) Jon J. Hangeland et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS