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Lead Optimization Computational Protocol at PDB Scale to Rationally Optimize Attachments to a Given Kinase Inhibitor Scaffold
Moriaud F., Henry T., Adcock S.A., Vorotynsev A.M., Martin L., Doppelt O.

We’ve used MED-SuMo to query and mine the Protein’s Surface Chemical Functions surrounding fragments of PDB ligands, seeking similarities with the kinase of interest (Vegfr DFGout, pdb code 2oh4, ligand code GIG) and collecting a library of 1129 unique fragments positioned in the vegfr’s active site and annotated with the counts of contacts and h-bonds. With them we optimize a substructure of the GIG ligand to find others DFGout ligands.

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New Developments for a Full Automation of the FIP Beamline at the ESRF
Jacquamet L., Bertoni A., Borel F., Charrault P., Israel-Gouy P., Iwema T., Kahn R., Joly J., Ohana J., Pirocchi M., Robin A., Serre L., Vernede X. and Ferrer J. L.

FIP (French beamline for the Investigation of Proteins) at the ESRF (European Synchrotron Radiation Facility) pushed developments in automation to reach a fully automated beamline. - The energy adjustment and beam optimization are completely automated. - The screening of the different protein crystals is ensured by a robotic system.In addition, this robot offers the possibility to analyze crystals directly as they grow in drops inside crystallization plates.

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Insights into the Mechanism of Partial Agonism: Crystal Structures of the Peroxisome Proliferator-activated Receptor-gamma Ligand-Binding Domain in the Complex with Two Enantiomeric Ligands
Giorgio Pochetti, Cristina Godio, Nico Mitro, Donatella Caruso, Samuele Scurati, Andrea Galmozzi, Fulvio Loiodice, Giuseppe Fracchiolla, Paolo Tortorella, Antonio Laghezza, Antonio Lavecchia, Ettore Novellino, Fernando Mazza, Maurizio Crestani

The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of glucose and lipid metabolism. They are activated by natural ligands, such as fatty acids, and are also target of synthetic antidiabetic and hypolipidemic drugs. By using cell-based reporter assays, we studied the transactivation activity of two enantiomeric ureidofibrate derivatives.

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Methods For Automated Structure Determination for Ligands Within a Protein-Ligand Complex
Gregory L. Warren and Matthew T. Stahl

Afitt is a software package for automated ligand conformation generation and placement within algorithmically identified unfilled electron density. Following real space refinement, the ligand solution is sent for subsequent refinement by Refmac or CNX, via coordinate and dictionary files. We have validated Afitt on forty publicly available data sets, chosen because it contains examples of highly strained ligand conformations.

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Automated, Low Volume Dynamic Light Scattering Technology to Accelerate Protein Crystallization
Kevin Jackson and Robert Collins

The quest for solving protein structure largely relies upon X-Ray diffraction, a method requiring crystalline forms of the target protein. Among the many steps comprising structure determination, the process of protein crystallization represents one of the most significant, time-consuming challenges. A new low sample volume, automated dynamic light scattering (DLS) technology has been developed – the DynaPro Plate Reader.

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A Solution for Low Volume Pipetting Applications Requiring High Accuracy of Sample Placement
Joby Jenkins, Rob Lewis, Tristan Cope and Chloë Milburn

Mosquito’s unique positive displacement disposable tips and precise X, Y and Z movements allow smaller drops with accurate and repeatable volumes to be positioned very precisely. This ability is essential for successful assay miniaturisation and the set-up of more effective serial dilutions or protein crystallography screens.

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Facilitating Low Volume Protein Crystallography Set-ups Using the Mosquito® Liquid Handler
Jas Sanghera, Joby Jenkins, Rob Lewis, Chloe Milburn

The mosquito® (TTP LabTech) offers fast positive displacement pipettingfor accurate and reproducible aspiration and dispensing throughout the 50 nL-1.2 µL range, producing CVs of <8% at 50 nLirrespective of viscosity. Mosquito’s micropipettes are also disposable, thus guaranteeing zero cross-contamination where required.

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From Medicinal Plants to Bioactive Drugs
Ilaria Lampronti, Mahmud T.H. Khan, Antoine M. Saab, Elisabetta Lambert, Letizia Penolazzi, Roberta Piva and Roberto Gambari

The aim of our study was to analyze the antiproliferative activity effects on human tumor cell lines and the differentiating activity on human erythroleukemic K562 cells of different extracts derived from medicinal plants of Bangladesh and Lebanon.

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Rapid and Miniaturized Robotic Crystallization Experiment using the Honeybee 963™ System
Malcolm Willson, Hamid Khoja and Charles Dang

The Honeybee 963 for automated sitting drop crystallization studies enables rapid, precise and accurate dispensing of nano-liter (nl) volumes of screening and protein solutions. Rapid dispensing to both reservoirs and shelves minimizes evaporation while precise and accurate dispensing allows for miniaturization and conserves precious protein.

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Showing Results 21 - 30 of 31
Scientific News
Crouching Protein, Hidden Enzyme
A new study led by scientists at The Scripps Research Institute (TSRI) and the University of California (UC), Berkeley shows how a crucial molecular enzyme starts in a tucked-in somersault position and flips out when it encounters the right target.
3D Images of Enzymes May Lead to Improved Antibiotics
Research advances understanding of how crucial proteins function.
Supply Chain
Chemists discover how a single enzyme maintains a cell’s pool of DNA building blocks.
Seeing DROSHA for the First Time
IBS team gets the first glimpse of elusive protein structure.
Scientists Blueprint Tiny Cellular ‘Nanomachine’
Scientists have drawn up molecular blueprints of a tiny cellular ‘nanomachine’, whose evolution is an extraordinary feat of nature, by using one of the brightest X-ray sources on Earth.
Pioneering Brain Cancer Technique Could Lead to Better Prognosis for Patients
4,000th paper published from Diamond research could improve outcomes for brain cancer sufferers.
Big Moves in Protein Structure Prediction and Design
Custom design with atomic level accuracy enables researchers to craft a whole new world of proteins.
Pushing Drug Discovery Forward
A new study, led by scientists at The Scripps Research Institute (TSRI), shows how different pharmaceutical drugs hit either the “on” or “off” switch of a signaling protein linked to asthma, obesity and type 2 diabetes.
Solved Structure of S. pneumoniae Enzyme Could Lead to New Antibiotics
Scientists solve structure of a key bacterial enzyme from streptococcus pneumoniae: a major cause of bacterial meningitis, bronchitis, ear infection and pneumonia.
A New Way to Look at MOFs
International study challenges prevailing view on how metal organic frameworks store gases.
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