The DINGO dataset: a comprehensive set of data for the SAMPL challenge

Part of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers’ work, a reasonably comprehensive set of data was collected using a number of techniques. These included surface plasmon resonance, isothermal titration calorimetry, protein crystallization and protein crystallography. Using these techniques we could determine the kinetics of fragment binding, the energy of binding, how this affects the ability of the target to crystallize, and when the fragment did bind, the pose or orientation of binding. Both the final data set and all of the raw images have been made available to the community for scrutiny and further work. This overview sets out to give the parameters of the experiments done and what might be done differently for future studies

The cryo-electron microscopy supramolecular structure of the bacterial stressosome unveils its mechanism of activation

How the stressosome, the epicenter of the stress response in bacteria, transmits stress signals from the environment has remained elusive. The stressosome consists of multiple copies of three proteins RsbR, RsbS and RsbT, a kinase that is important for its activation. Using cryo-electron microscopy, we determined the atomic organization of the Listeria monocytogenes stressosome at 3.38 Å resolution. RsbR and RsbS are organized in a 60-protomers truncated icosahedron. A key phosphorylation site on RsbR (T209) is partially hidden by an RsbR flexible loop, whose "open" or "closed" position could modulate stressosome activity. Interaction between three glutamic acids in the N-terminal domain of RsbR and the membrane-bound mini-protein Prli42 is essential for Listeria survival to stress. Together, our data provide the atomic model of the stressosome core and highlight a loop important for stressosome activation, paving the way towards elucidating the mechanism of signal transduction by the stressosome in bacteria

Measurement of electrons from beauty-hadron decays in p-Pb collisions at root(NN)-N-S=5.02 TeV and Pb-Pb collisions at. root(NN)-N-S=2.76 TeV

The production of beauty hadrons was measured via semi-leptonic decays at mid-rapidity with the ALICE detector at the LHC in the transverse momentum interval 1<pT< 8 GeV/c in minimum-bias p-Pb collisions at sNN=5.02 TeV and in 1.3 < pT< 8 GeV/c in the 20% most central Pb-Pb collisions at sNN=2.76 TeV. The pp reference spectra at sNN=5.02 TeV and s=2.76 TeV, needed for the calculation of the nuclear modification factors RpPb and RPbPb, were obtained by a pQCD-driven scaling of the cross section of electrons from beauty-hadron decays measured at s=7 TeV. In the pT interval 3 < pT< 8 GeV/c, a suppression of the yield of electrons from beauty-hadron decays is observed in Pb-Pb compared to pp collisions. Towards lower pT, the RPbPb values increase with large systematic uncertainties. The RpPb is consistent with unity within systematic uncertainties and is well described by theoretical calculations that include cold nuclear matter effects in p-Pb collisions. The measured RpPb and these calculations indicate that cold nuclear matter effects are small at high transverse momentum also in Pb-Pb collisions. Therefore., the observed reduction of RPbPb below unity at high pT may be ascribed to an effect of the hot and dense medium formed in Pb-Pb collisions.[Figure not available: see fulltext.

OEChem – Python Theory Manual Version 1.5.1

of copyright notice is precautionary only and does not imply publication or disclosure. The information supplied in this document is believed to be true but no liability is assumed for its use or the infringement of the rights of others resulting from its use. Information in this document is subject to change without notice and does not represent a commitment on the part of OpenEye Scientific Software. This package is sold/licensed/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without OpenEye Scientific Software’s prior consent, in any form of packaging or cover other than that in which it was produced. No part of this manual or accompanying documentation, may be reproduced, stored in a retrieval system on optical or magnetic disk, tape, CD, DVD or other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying recording or otherwise for any purpose other than for the purchaser’s personal use without a legal agreement or other written permission granted by OpenEye. This product should not be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or communication of aircraft or ground support equipment. OpenEye Scientific software, shall not be liable, in whole or in part, for any claims arising from such use, including death, bankruptcy or outbreak of war. Windows is a registered trademark of Microsoft Corporation. Apple and Macintosh are registered trademarks of Apple Computer, Inc. AIX and IBM are registered trademarks of International Business Machines Corporation. UNIX is a registered trademark of the Open Group. RedHat is a registered trademark of RedHat, Inc. Linux is a registered trademark of Linus Torvalds. Alpha is a trademark of Digita

OEChem – C++ Theory Manual Version 1.5.1

of copyright notice is precautionary only and does not imply publication or disclosure. The information supplied in this document is believed to be true but no liability is assumed for its use or the infringement of the rights of others resulting from its use. Information in this document is subject to change without notice and does not represent a commitment on the part of OpenEye Scientific Software. This package is sold/licensed/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without OpenEye Scientific Software’s prior consent, in any form of packaging or cover other than that in which it was produced. No part of this manual or accompanying documentation, may be reproduced, stored in a retrieval system on optical or magnetic disk, tape, CD, DVD or other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying recording or otherwise for any purpose other than for the purchaser’s personal use without a legal agreement or other written permission granted by OpenEye. This product should not be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or communication of aircraft or ground support equipment. OpenEye Scientific software, shall not be liable, in whole or in part, for any claims arising from such use, including death, bankruptcy or outbreak of war. Windows is a registered trademark of Microsoft Corporation. Apple and Macintosh are registered trademarks of Apple Computer, Inc. AIX and IBM are registered trademarks of International Business Machines Corporation. UNIX is a registered trademark of the Open Group. RedHat is a registered trademark of RedHat, Inc. Linux is a registered trademark of Linus Torvalds. Alpha is a trademark of Digita