Search Results - "GEDECK, Peter"

Comparability of mixed IC₅₀ data - a statistical analysis by Kalliokoski, Tuomo, Kramer, Christian, Vulpetti, Anna, Gedeck, Peter

“…The biochemical half maximal inhibitory concentration (IC50) is the most commonly used metric for on-target activity in lead optimization. It is used to guide…”
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A Cryptosporidium PI(4)K inhibitor is a drug candidate for cryptosporidiosis by Manjunatha, Ujjini H., Vinayak, Sumiti, Zambriski, Jennifer A., Chao, Alexander T., Sy, Tracy, Noble, Christian G., Bonamy, Ghislain M. C., Kondreddi, Ravinder R., Zou, Bin, Gedeck, Peter, Brooks, Carrie F., Herbert, Gillian T., Sateriale, Adam, Tandel, Jayesh, Noh, Susan, Lakshminarayana, Suresh B., Lim, Siau H., Goodman, Laura B., Bodenreider, Christophe, Feng, Gu, Zhang, Lijun, Blasco, Francesca, Wagner, Juergen, Leong, F. Joel, Striepen, Boris, Diagana, Thierry T.

“…Diarrhoeal disease is responsible for 8.6% of global child mortality. Recent epidemiological studies found the protozoan parasite Cryptosporidium to be a…”
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Matched Molecular Pair Analysis: Significance and the Impact of Experimental Uncertainty by Kramer, Christian, Fuchs, Julian E, Whitebread, Steven, Gedeck, Peter, Liedl, Klaus R

“…Matched molecular pair analysis (MMPA) has become a major tool for analyzing large chemistry data sets for promising chemical transformations. However, the…”
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Mutations in the Plasmodium falciparum Cyclic Amine Resistance Locus (PfCARL) Confer Multidrug Resistance by LaMonte, Gregory, Lim, Michelle Yi-Xiu, Wree, Melanie, Reimer, Christin, Nachon, Marie, Corey, Victoria, Gedeck, Peter, Plouffe, David, Du, Alan, Figueroa, Nelissa, Yeung, Bryan, Bifani, Pablo, Winzeler, Elizabeth A

“…Mutations in the Plasmodium falciparum cyclic amine resistance locus (PfCARL) are associated with parasite resistance to the imidazolopiperazines, a potent…”
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Drug block of the hERG potassium channel: Insight from modeling by Stansfeld, Phillip J., Gedeck, Peter, Gosling, Martin, Cox, Brian, Mitcheson, John S., Sutcliffe, Michael J.

“…Many commonly used, structurally diverse, drugs block the human ether‐a‐go‐go‐related gene (hERG) K+ channel to cause acquired long QT syndrome, which can lead…”
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Capturing mixture composition: an open machine-readable format for representing mixed substances by Clark, Alex M., McEwen, Leah R., Gedeck, Peter, Bunin, Barry A.

“…We describe a file format that is designed to represent mixtures of compounds in a way that is fully machine readable. This Mixfile format is intended to fill…”
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UDP-galactose and acetyl-CoA transporters as Plasmodium multidrug resistance genes by Lim, Michelle Yi-Xiu, LaMonte, Gregory, Lee, Marcus C. S., Reimer, Christin, Tan, Bee Huat, Corey, Victoria, Tjahjadi, Bianca F., Chua, Adeline, Nachon, Marie, Wintjens, René, Gedeck, Peter, Malleret, Benoit, Renia, Laurent, Bonamy, Ghislain M. C., Ho, Paul Chi-Lui, Yeung, Bryan K. S., Chow, Eric D., Lim, Liting, Fidock, David A., Diagana, Thierry T., Winzeler, Elizabeth A., Bifani, Pablo

“…A molecular understanding of drug resistance mechanisms enables surveillance of the effectiveness of new antimicrobial therapies during development and…”
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Using Machine Learning to Parse Chemical Mixture Descriptions by Clark, Alex M, Gedeck, Peter, Cheung, Philip P, Bunin, Barry A

“…Chemical mixtures have recently come to the attention of open standards and data structures for capturing machine-readable descriptions for informatics uses…”
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Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets by Kramer, Christian, Gedeck, Peter

“…With the emergence of large collections of protein−ligand complexes complemented by binding data, as found in PDBbind or BindingMOAD, new opportunities for…”
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The Experimental Uncertainty of Heterogeneous Public K i Data by Kramer, Christian, Kalliokoski, Tuomo, Gedeck, Peter, Vulpetti, Anna

“…The maximum achievable accuracy of in silico models depends on the quality of the experimental data. Consequently, experimental uncertainty defines a natural…”
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Atomic multipoles: Electrostatic potential fit, local reference axis systems, and conformational dependence by Kramer, Christian, Gedeck, Peter, Meuwly, Markus

“…Currently, all standard force fields for biomolecular simulations use point charges to model intermolecular electrostatic interactions. This is a fast and…”
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Developing Collaborative QSAR Models Without Sharing Structures by Gedeck, Peter, Skolnik, Suzanne, Rodde, Stephane

“…It is widely understood that QSAR models greatly improve if more data are used. However, irrespective of model quality, once chemical structures diverge too…”
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Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters by Kramer, Christian, Gedeck, Peter, Meuwly, Markus

“…Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically…”
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Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors by Kramer, Christian, Gedeck, Peter

“…Scoring functions for protein−ligand docking have received much attention in the past two decades. In many cases, remarkable success has been demonstrated in…”
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Three Descriptor Model Sets a High Standard for the CSAR-NRC HiQ Benchmark by Kramer, Christian, Gedeck, Peter

“…Here we report the results we obtained with a proteochemometric approach for predicting ligand binding free energies of the CSAR-NRC HiQ benchmark data set…”
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Prediction of pK a Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines by Lu, Yipin, Anand, Shankara, Shirley, William, Gedeck, Peter, Kelley, Brian P, Skolnik, Suzanne, Rodde, Stephane, Nguyen, Mai, Lindvall, Mika, Jia, Weiping

“…The acid–base dissociation constant, pK a, is a key parameter to define the ionization state of a compound and directly affects its biopharmaceutical profile…”
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QSAR − How Good Is It in Practice? Comparison of Descriptor Sets on an Unbiased Cross Section of Corporate Data Sets by Gedeck, Peter, Rohde, Bernhard, Bartels, Christian

“…The quality of QSAR (Quantitative Structure−Activity Relationships) predictions depends on a large number of factors including the descriptor set, the…”
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Computational Chemistry at Novartis by Richard Lewis, Peter Ertl, Edgar Jacoby, Marina Tintelnot-Blomley, Peter Gedeck, Romain M. Wolf, Manuel C. Peitsch

“…Computational approaches have become an integral part of modern drug discovery and medicinal chemistry. These approaches can be roughly classified into…”
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Deriving Static Atomic Multipoles from the Electrostatic Potential by Kramer, Christian, Bereau, Tristan, Spinn, Alexander, Liedl, Klaus R, Gedeck, Peter, Meuwly, Markus

“…The description of molecular systems using multipolar electrostatics calls for automated methods to fit the necessary parameters. In this paper, we describe an…”
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Prediction of pKa Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines by Lu, Yipin, Anand, Shankara, Shirley, William, Gedeck, Peter, Kelley, Brian P, Skolnik, Suzanne, Rodde, Stephane, Nguyen, Mai, Lindvall, Mika, Jia, Weiping

“…The acid–base dissociation constant, pKa, is a key parameter to define the ionization state of a compound and directly affects its biopharmaceutical profile…”
Get full text