Drug design for ever, from hype to hope

Integrating GPCR-specific information with full text articles

(2011) Bas Vroling et al.   BMC BIOINFORMATICS

Machine learning study for the prediction of transdermal peptide

(2011) Eunkyoung Jung et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking and quantitative structure–activity relationship studies for 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2,3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors

(2011) Julio Caballero et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases

(2011) Ivano Eberini et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors

(2011) Petr Dobeš et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase

(2011) Jakyung Yoo et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure-guided fragment-based in silico drug design of dengue protease inhibitors

(2011) Tim Knehans et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structural biology: Breaking the protein rules

(2011) Tanguy Chouard   NATURE

Structure and function of an irreversible agonist-β2 adrenoceptor complex

(2011) Daniel M. Rosenbaum et al.   NATURE

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis

(2011) An Cerdobbel et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Incorporation of evolutionary information into Rosetta comparative modeling

(2011) James Thompson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

(2011) Randy J. Read et al.   STRUCTURE

Understanding protein non-folding

(2010) Vladimir N. Uversky et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces

(2010) Hanka Venselaar et al.   BMC BIOINFORMATICS

The α/β-Hydrolase Fold 3DM Database (ABHDB) as a Tool for Protein Engineering

(2010) Robert Kourist et al.   CHEMBIOCHEM

Novel tools for extraction and validation of disease-related mutations applied to fabry disease

(2010) Remko Kuipers et al.   HUMAN MUTATION

Trainable structure–activity relationship model for virtual screening of CYP3A4 inhibition

(2010) Remigijus Didziapetris et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach

(2010) Marco A. C. Neves et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function

(2010) Daniel P. Garden et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Conserved Binding Mode of Human β2Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

(2010) Daniel Wacker et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

(2009) Robbie P. Joosten et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Calling International Rescue: knowledge lost in literature and data landslide!

(2009) Teresa K. Attwood et al.   BIOCHEMICAL JOURNAL

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

(2009) Robbie P. Joosten et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

CAUTION: Popular “Benchmark” Data Sets Do Not Distinguish the Merits of 3D QSAR Methods

(2009) John Manchester et al.   Journal of Chemical Information and Modeling

Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?

(2009) Pablo Englebienne et al.   Journal of Chemical Information and Modeling

Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists

(2009) Bjoern A. Krueger et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

(2009) Ajay N. Jain   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

DFT-based QSAR and QSPR models of several cis-platinum complexes: solvent effect

(2009) Pubalee Sarmah et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8

(2009) Elmar Krieger et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A ligand’s-eye view of protein binding

(2008) Robert D. Clark   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

(2008) Giovanni Bottegoni et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An improved adaptive genetic algorithm for protein–ligand docking

(2008) Ling Kang et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An improved scoring function for suboptimal polar ligand complexes

(2008) Giovanni Cincilla et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

(2008) Kavitha Bharatham et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

What induces pocket openings on protein surface patches involved in protein–protein interactions?

(2008) Susanne Eyrisch et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

QSAR: dead or alive?

(2008) Arthur M. Doweyko   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Community benchmarks for virtual screening

(2008) John J. Irwin   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

PK/PD Modelling and Beyond: Impact on Drug Development

(2008) Douwe D. Breimer   PHARMACEUTICAL RESEARCH

Conformational thermostabilization of the  1-adrenergic receptor in a detergent-resistant form

(2008) M. J. Serrano-Vega et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Docking and scoring with alternative side-chain conformations

(2008) Christoph Hartmann et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS