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Publications

Changing Paradigms in Drug Discovery: Scientific Business Intelligence™ and Workflow Solutions

Abstract: Workflow solutions driven by data pipelining are increasingly becoming popular for accessing, aggregating and analyzing disparate data to make informed and intelligent decisions. Uses of workflow technologies which facilitate business intelligence (BI) improve productivity, decision making and research efficiency. In order to provide BI in a scientific or clinical based organization, it is imperative that the application or workflow technology must be compatible with multiple data types and formats, be able to analyze the data and make it available throughout the organization. We term this as Scientific Business Intelligence (SBI) and discuss how modeling, simulations and informatics software, integrated with open and standards-based scientific operating platform (SOP), can deliver scientifically-relevant BI solutions. We illustrate SBI with several examples encompassing all levels of users within an organization.

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Validation Studies of the Site-Directed Docking Program LibDock

This joint publication between GlaxoSmithKline and Accelrys shows LibDock is one of the top performers among ten docking programs (Glide, GOLD, FlexX, Fred, MOE, Dock4, and others) when applied to eight receptor targets. Specific successes with LibDock include:

  • Best recovery of X-ray pose for HCV Polymerase and Factor Xa
  • Best enrichment of actives after within 10% of scored compounds in a virtual screening experiment with Gyrase B Isomerase

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Review of Pattern Recognition Techniques (including those in QUANTA)

"Statistical Pattern Recognition for Macromolecular Crystallographers,"a review article that discusses pattern-recognition techniques within popular model-building packages, including QUANTA. The reviewer states that, at present, QUANTA offers the best tools in this field, saying, "The efficient implementation allows fast execution, and this combined with the interactive graphics capabilities makes QUANTA perhaps overall one of the most advanced model-building tools currently available." ( Acta Crystallogr. Sect: D Biol. Crystallogr. , 2004, 60 , 2133-2143.)
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Crystal Growth Morphology Prediction for Organic Crystals: a Systematic Study of the Dependence of Predicted Morphology on Choice of Force Fields (Technical Paper)

Materials Studio Morphology allows you to predict crystal morphology from the atomic structure of a crystal. Morphology allows the prediction of crystal shape, the development of tailor-made additives, and the control of solvent and impurity effects. Morphology's application areas include pharmaceuticals, agrochemicals, food sciences, petrochemicals, cements, and commodity and specialty chemicals. This paper reports the results of a systematic study of the dependence of the growth morphology predictions on the use of specific force fields on five organic systems. The ability of each force field to reproduce the crystal structure and lattice energy was also considered as the criteria for suitability for modeling the condensed phases of the systems of interest.
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Quinoline binding site on malaria pigment crystal: A rational pathway for antimalaria drug design

The paper outlines how researchers at the Weizmann Institute of Science, Israel, and Transform Pharmaceuticals, Cambridge, MA, used crystal morphology-predicting software tools to model the crystal formation of the malaria pigments crystals, the by-products of hemoglobin digestion by the malaria parasite, and used this information to propose binding sites for quinoline-based anti-malarial drugs.
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Electrostatics in Organic Crystals Paper

Receive a copy of the paper, “A study of different approaches to the electrostatic interaction in force field methods for organic crystals” by S. Brodersen, S. Wilke, F. J. J. Leusen and G. Engel.
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Accord – Advanced Stereochemical Representation / Cheminformatics (Technical Paper)

The Accord range of cheminformatics software, well known to provide flexible, advanced stereochemistry support, has enhanced its stereochemical representation. This paper reviews a number of key issues in the representation of stereochemistry, and shows how they have been addressed within the Accord Chemistry Engine.
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